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Showing metabocard for Biliverdin (HMDB0001008)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (5) Show 5 proteinsXML
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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-07-12 23:05:07 UTC
HMDB IDHMDB0001008
Secondary Accession Numbers
  • HMDB0002309
  • HMDB01008
  • HMDB02309
Metabolite Identification
Common NameBiliverdin
DescriptionBiliverdin is a green pigment formed as a byproduct of hemoglobin breakdown. It consists of four linearly connected pyrrole rings (a tetrapyrrole). Biliverdin is formed when the heme group in hemoglobin is cleaved at its alpha-methene bridge. The resulting biliverdin is then reduced to bilirubin, a yellow pigment, by the enzyme biliverdin reductase. The changing color of a bruise from deep purple to yellow over time is a graphical indicator of this reaction. Biliverdin occurs in the bile of amphibia and of birds, but not in normal human bile or serum.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001008 (Biliverdin)

  Mrv1652309042000172D          

 43 46  0  0  0  0            999 V2000
    1.8296   -1.3329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7497   -2.1176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0846   -2.1176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8692   -2.3725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4171   -2.6025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0858    1.0802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9790    0.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1720    0.2597    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8395    1.4156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0110    2.2227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3914    0.8026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2120    0.8889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5475    1.6425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3713    1.4927    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8196   -2.1176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1544   -2.1176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4870   -3.4275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4171   -5.0775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  6 39  1  0  0  0  0
 15  7  2  0  0  0  0
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  8 37  2  0  0  0  0
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 12  8  1  0  0  0  0
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 18 16  1  0  0  0  0
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 39 40  1  0  0  0  0
 40 42  1  0  0  0  0
 42 41  1  0  0  0  0
 42 43  2  0  0  0  0
M  END
Download

3D MOL for HMDB0001008 (Biliverdin)

HMDB0001008
     RDKit          3D
Biliverdin
 77 80  0  0  0  0  0  0  0  0999 V2000
    6.8895    5.7479    0.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8941    5.2566   -0.2359 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2939    3.9620    0.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2878    3.3809   -0.5008 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5894    3.9652   -1.6807 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9446    2.0975    0.1149 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9300    1.3295   -0.1104 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5373    0.0648    0.4221 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2928   -0.3555    0.1510 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0380   -1.5939    0.7052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1195   -2.2440    0.5866 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.7056    3.1106    1.2018 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.3080    5.2370    1.2712 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3291   -4.2171    0.5015 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5562   -4.5402    0.6160 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.1924   -0.7493    0.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.8558    1.1976    1.8593 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
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  4  5  1  0
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  6  7  2  0
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 13 14  1  0
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 18 20  1  0
 20 21  1  0
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 22 23  1  0
 23 24  2  3
 14 25  2  0
 25 26  1  0
 25 27  1  0
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 33 34  1  0
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  6 41  1  0
 41 42  1  0
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 39  8  1  0
 27 12  2  0
 22 16  1  0
  1 44  1  0
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  2 46  1  0
  5 47  1  0
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  7 50  1  0
 11 51  1  0
 13 52  1  0
 15 53  1  0
 17 54  1  0
 21 55  1  0
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 35 71  1  0
 35 72  1  0
 38 73  1  0
 40 74  1  0
 40 75  1  0
 40 76  1  0
 41 77  1  0
M  END
Download

3D SDF for HMDB0001008 (Biliverdin)

  Mrv1652309042000172D          

 43 46  0  0  0  0            999 V2000
    1.8296   -1.3329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7497   -2.1176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0046   -1.3329    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0846   -2.1176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8692   -2.3725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4171   -2.6025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0858    1.0802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9790    0.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1720    0.2597    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8395    1.4156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0110    2.2227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3914    0.8026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2120    0.8889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5475    1.6425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3713    1.4927    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8196   -2.1176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8995   -1.3329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0745   -1.3329    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1544   -2.1176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9391   -2.3725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4870   -2.6025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4870   -3.4275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2014   -3.8400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4870   -5.0775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2014   -4.6650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9159   -5.0775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0349   -2.3725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0489    0.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4613    0.8026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2818    0.8889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9093    1.4156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0809    2.2227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8655    2.4775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2419    0.2597    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1556    1.0802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4412    1.4927    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3146   -0.6655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3844   -0.6655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4171   -3.4275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1316   -3.8400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8460   -5.0775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1316   -4.6650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4171   -5.0775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 37  1  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  2  0  0  0  0
  6  2  2  0  0  0  0
  3  2  1  0  0  0  0
  2 27  1  0  0  0  0
  4  6  1  0  0  0  0
  4  5  1  0  0  0  0
  6 39  1  0  0  0  0
 15  7  2  0  0  0  0
  7  9  1  0  0  0  0
 10  7  1  0  0  0  0
  8 37  2  0  0  0  0
  9  8  1  0  0  0  0
 12  8  1  0  0  0  0
 10 12  2  0  0  0  0
 10 11  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 16 27  2  0  0  0  0
 18 16  1  0  0  0  0
 21 16  1  0  0  0  0
 38 17  1  0  0  0  0
 18 17  2  0  0  0  0
 19 17  1  0  0  0  0
 19 21  2  0  0  0  0
 19 20  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 25  1  0  0  0  0
 25 24  1  0  0  0  0
 25 26  2  0  0  0  0
 28 34  1  0  0  0  0
 29 28  1  0  0  0  0
 38 28  2  0  0  0  0
 31 29  2  0  0  0  0
 29 30  1  0  0  0  0
 31 35  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 39 40  1  0  0  0  0
 40 42  1  0  0  0  0
 42 41  1  0  0  0  0
 42 43  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001008

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=C(C=C)\C(NC1=O)=C\C1=C(C)C(CCC(O)=O)=C(N1)\C=C1/N=C(/C=C2\NC(=O)C(C=C)=C2C)C(C)=C1CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C33H34N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-15,35H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,28-15-

> <INCHI_KEY>
QBUVFDKTZJNUPP-BBROENKCSA-N

> <FORMULA>
C33H34N4O6

> <MOLECULAR_WEIGHT>
582.657

> <EXACT_MASS>
582.247834831

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
64.76179351109342

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(2-{[(2Z)-3-(2-carboxyethyl)-5-{[(2Z)-4-ethenyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-ylidene]methyl}-4-methyl-2H-pyrrol-2-ylidene]methyl}-5-{[(2Z)-3-ethenyl-4-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-ylidene]methyl}-4-methyl-1H-pyrrol-3-yl)propanoic acid

> <ALOGPS_LOGP>
3.44

> <JCHEM_LOGP>
0.5727987549162802

> <ALOGPS_LOGS>
-4.65

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.462128056457106

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.868581374117636

> <JCHEM_PKA_STRONGEST_BASIC>
5.8592066222604196

> <JCHEM_POLAR_SURFACE_AREA>
160.95

> <JCHEM_REFRACTIVITY>
169.35510000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.29e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
biliverdine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001008 (Biliverdin)

HMDB0001008
     RDKit          3D
Biliverdin
 77 80  0  0  0  0  0  0  0  0999 V2000
    6.8895    5.7479    0.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8941    5.2566   -0.2359 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2939    3.9620    0.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2878    3.3809   -0.5008 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5894    3.9652   -1.6807 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9446    2.0975    0.1149 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9300    1.3295   -0.1104 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5373    0.0648    0.4221 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2928   -0.3555    0.1510 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0380   -1.5939    0.7052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1195   -2.2440    0.5866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1804   -1.6049   -0.1798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6126   -0.3396   -0.0815 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5565   -0.0768   -0.9589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3664    1.1171   -1.2328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9791    1.7860   -0.2605 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.7704    2.2509    3.1090 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1690    3.2594    0.9168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0192    4.3981    1.3127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8013    2.9830   -0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1839    3.7476   -1.4989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9538    3.6592   -2.7459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7907   -1.2251   -1.7109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7319   -1.4060   -2.8421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9216   -2.1836   -1.2136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7745   -3.5463   -1.7177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2802   -4.6589   -0.8691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7028   -4.6532   -0.5428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5520   -3.8033   -0.8763 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1456   -5.7503    0.2455 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2393   -1.9994    1.3770 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4405   -3.2534    2.1497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4745   -4.4177    1.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6798   -5.6846    1.9427 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8101   -5.6475    3.1763 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7212   -6.8696    1.2583 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1226   -0.9876    1.1834 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5319   -1.2137    1.6474 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8480    1.9449    1.1891 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7056    3.1106    1.2018 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6168    3.2432    2.0608 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3080    5.2370    1.2712 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2831    6.6979    0.1364 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4744    5.8068   -1.1007 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5174    3.6379   -1.6354 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0676    3.5276   -2.5892 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6452    5.0631   -1.6708 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2454    1.7749   -0.8993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2589   -3.1998    1.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2174    0.3611    0.6157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4818    1.4823   -2.2309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3523    0.5263    1.4494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3400    5.2743    1.5093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5946    4.2067    2.2470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7655    4.6772    0.5507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8422    4.6358   -1.2441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3899    2.9605   -3.2862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4319    4.4611   -3.3880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7366   -1.7226   -2.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8082   -0.4354   -3.4258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3152   -2.1190   -3.6173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3095   -3.6423   -2.7066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7109   -3.7833   -1.9892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0912   -5.6238   -1.4342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6558   -4.7805    0.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2993   -6.6038   -0.2961 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5925   -3.3628    2.8875 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3907   -3.2064    2.7116 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3291   -4.2171    0.5015 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5562   -4.5402    0.6160 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9731   -7.7745    1.6461 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7428   -2.3353    1.5830 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1924   -0.7493    0.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6544   -0.8830    2.6764 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8558    1.1976    1.8593 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
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 16 17  1  0
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 18 20  1  0
 20 21  1  0
 20 22  2  0
 22 23  1  0
 23 24  2  3
 14 25  2  0
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 25 27  1  0
 27 28  1  0
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 29 30  1  0
 30 31  2  0
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 10 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  2  0
 36 38  1  0
 33 39  2  0
 39 40  1  0
  6 41  1  0
 41 42  1  0
 42 43  2  0
 42  3  1  0
 39  8  1  0
 27 12  2  0
 22 16  1  0
  1 44  1  0
  1 45  1  0
  2 46  1  0
  5 47  1  0
  5 48  1  0
  5 49  1  0
  7 50  1  0
 11 51  1  0
 13 52  1  0
 15 53  1  0
 17 54  1  0
 21 55  1  0
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 35 71  1  0
 35 72  1  0
 38 73  1  0
 40 74  1  0
 40 75  1  0
 40 76  1  0
 41 77  1  0
M  END
Download

PDB for HMDB0001008 (Biliverdin)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       3.415  -2.488   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.399  -3.953   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.875  -2.488   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       3.891  -3.953   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.356  -4.429   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.645  -4.858   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.027   2.016   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.694   0.165   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.188   0.485   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.434   2.642   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.754   4.149   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.464   1.498   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.996   1.659   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.622   3.066   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.693   2.786   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.530  -3.953   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.546  -2.488   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      -2.006  -2.488   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0      -4.022  -3.953   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.486  -4.429   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.776  -4.858   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.776  -6.398   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -4.109  -7.168   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -2.776  -9.478   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -4.109  -8.708   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -5.443  -9.478   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -0.065  -4.429   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -3.825   0.165   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -4.594   1.498   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -6.126   1.659   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.564   2.642   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.884   4.149   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.349   4.625   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      -2.318   0.485   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0      -2.157   2.016   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -0.824   2.786   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       4.321  -1.242   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -4.451  -1.242   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       2.645  -6.398   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       3.979  -7.168   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       5.313  -9.478   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0       3.979  -8.708   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0       2.645  -9.478   0.000  0.00  0.00           O+0
CONECT    1   37    3    4                                                  
CONECT    2    6    3   27                                                  
CONECT    3    1    2                                                       
CONECT    4    1    6    5                                                  
CONECT    5    4                                                            
CONECT    6    2    4   39                                                  
CONECT    7   15    9   10                                                  
CONECT    8   37    9   12                                                  
CONECT    9    7    8                                                       
CONECT   10    7   12   11                                                  
CONECT   11   10                                                            
CONECT   12    8   10   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15    7                                                            
CONECT   16   27   18   21                                                  
CONECT   17   38   18   19                                                  
CONECT   18   16   17                                                       
CONECT   19   17   21   20                                                  
CONECT   20   19                                                            
CONECT   21   16   19   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22   25                                                       
CONECT   24   25                                                            
CONECT   25   23   24   26                                                  
CONECT   26   25                                                            
CONECT   27    2   16                                                       
CONECT   28   34   29   38                                                  
CONECT   29   28   31   30                                                  
CONECT   30   29                                                            
CONECT   31   29   35   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32                                                            
CONECT   34   28   35                                                       
CONECT   35   31   34   36                                                  
CONECT   36   35                                                            
CONECT   37    1    8                                                       
CONECT   38   17   28                                                       
CONECT   39    6   40                                                       
CONECT   40   39   42                                                       
CONECT   41   42                                                            
CONECT   42   40   41   43                                                  
CONECT   43   42                                                            
MASTER        0    0    0    0    0    0    0    0   43    0   92    0
END
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3D PDB for HMDB0001008 (Biliverdin)

COMPND    HMDB0001008
HETATM    1  C1  UNL     1       6.890   5.748   0.441  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.894   5.257  -0.236  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.294   3.962   0.117  1.00  0.00           C  
HETATM    4  C4  UNL     1       4.288   3.381  -0.501  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.589   3.965  -1.681  1.00  0.00           C  
HETATM    6  C6  UNL     1       3.945   2.097   0.115  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.930   1.330  -0.110  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.537   0.065   0.422  1.00  0.00           C  
HETATM    9  N1  UNL     1       1.293  -0.355   0.151  1.00  0.00           N  
HETATM   10  C9  UNL     1       1.038  -1.594   0.705  1.00  0.00           C  
HETATM   11  C10 UNL     1      -0.119  -2.244   0.587  1.00  0.00           C  
HETATM   12  C11 UNL     1      -1.180  -1.605  -0.180  1.00  0.00           C  
HETATM   13  N2  UNL     1      -1.613  -0.340  -0.081  1.00  0.00           N  
HETATM   14  C12 UNL     1      -2.556  -0.077  -0.959  1.00  0.00           C  
HETATM   15  C13 UNL     1      -3.366   1.117  -1.233  1.00  0.00           C  
HETATM   16  C14 UNL     1      -3.979   1.786  -0.260  1.00  0.00           C  
HETATM   17  N3  UNL     1      -3.875   1.365   1.097  1.00  0.00           N  
HETATM   18  C15 UNL     1      -4.628   2.297   1.847  1.00  0.00           C  
HETATM   19  O1  UNL     1      -4.770   2.251   3.109  1.00  0.00           O  
HETATM   20  C16 UNL     1      -5.169   3.259   0.917  1.00  0.00           C  
HETATM   21  C17 UNL     1      -6.019   4.398   1.313  1.00  0.00           C  
HETATM   22  C18 UNL     1      -4.801   2.983  -0.349  1.00  0.00           C  
HETATM   23  C19 UNL     1      -5.184   3.748  -1.499  1.00  0.00           C  
HETATM   24  C20 UNL     1      -4.954   3.659  -2.746  1.00  0.00           C  
HETATM   25  C21 UNL     1      -2.791  -1.225  -1.711  1.00  0.00           C  
HETATM   26  C22 UNL     1      -3.732  -1.406  -2.842  1.00  0.00           C  
HETATM   27  C23 UNL     1      -1.922  -2.184  -1.214  1.00  0.00           C  
HETATM   28  C24 UNL     1      -1.775  -3.546  -1.718  1.00  0.00           C  
HETATM   29  C25 UNL     1      -2.280  -4.659  -0.869  1.00  0.00           C  
HETATM   30  C26 UNL     1      -3.703  -4.653  -0.543  1.00  0.00           C  
HETATM   31  O2  UNL     1      -4.552  -3.803  -0.876  1.00  0.00           O  
HETATM   32  O3  UNL     1      -4.146  -5.750   0.246  1.00  0.00           O  
HETATM   33  C27 UNL     1       2.239  -1.999   1.377  1.00  0.00           C  
HETATM   34  C28 UNL     1       2.440  -3.253   2.150  1.00  0.00           C  
HETATM   35  C29 UNL     1       2.474  -4.418   1.197  1.00  0.00           C  
HETATM   36  C30 UNL     1       2.680  -5.685   1.943  1.00  0.00           C  
HETATM   37  O4  UNL     1       2.810  -5.648   3.176  1.00  0.00           O  
HETATM   38  O5  UNL     1       2.721  -6.870   1.258  1.00  0.00           O  
HETATM   39  C31 UNL     1       3.123  -0.988   1.183  1.00  0.00           C  
HETATM   40  C32 UNL     1       4.532  -1.214   1.647  1.00  0.00           C  
HETATM   41  N4  UNL     1       4.848   1.945   1.189  1.00  0.00           N  
HETATM   42  C33 UNL     1       5.706   3.111   1.202  1.00  0.00           C  
HETATM   43  O6  UNL     1       6.617   3.243   2.061  1.00  0.00           O  
HETATM   44  H1  UNL     1       7.308   5.237   1.271  1.00  0.00           H  
HETATM   45  H2  UNL     1       7.283   6.698   0.136  1.00  0.00           H  
HETATM   46  H3  UNL     1       5.474   5.807  -1.101  1.00  0.00           H  
HETATM   47  H4  UNL     1       2.517   3.638  -1.635  1.00  0.00           H  
HETATM   48  H5  UNL     1       4.068   3.528  -2.589  1.00  0.00           H  
HETATM   49  H6  UNL     1       3.645   5.063  -1.671  1.00  0.00           H  
HETATM   50  H7  UNL     1       2.245   1.775  -0.899  1.00  0.00           H  
HETATM   51  H8  UNL     1      -0.259  -3.200   1.062  1.00  0.00           H  
HETATM   52  H9  UNL     1      -1.217   0.361   0.616  1.00  0.00           H  
HETATM   53  H10 UNL     1      -3.482   1.482  -2.231  1.00  0.00           H  
HETATM   54  H11 UNL     1      -3.352   0.526   1.449  1.00  0.00           H  
HETATM   55  H12 UNL     1      -5.340   5.274   1.509  1.00  0.00           H  
HETATM   56  H13 UNL     1      -6.595   4.207   2.247  1.00  0.00           H  
HETATM   57  H14 UNL     1      -6.766   4.677   0.551  1.00  0.00           H  
HETATM   58  H15 UNL     1      -5.842   4.636  -1.244  1.00  0.00           H  
HETATM   59  H16 UNL     1      -4.390   2.960  -3.286  1.00  0.00           H  
HETATM   60  H17 UNL     1      -5.432   4.461  -3.388  1.00  0.00           H  
HETATM   61  H18 UNL     1      -4.737  -1.723  -2.577  1.00  0.00           H  
HETATM   62  H19 UNL     1      -3.808  -0.435  -3.426  1.00  0.00           H  
HETATM   63  H20 UNL     1      -3.315  -2.119  -3.617  1.00  0.00           H  
HETATM   64  H21 UNL     1      -2.310  -3.642  -2.707  1.00  0.00           H  
HETATM   65  H22 UNL     1      -0.711  -3.783  -1.989  1.00  0.00           H  
HETATM   66  H23 UNL     1      -2.091  -5.624  -1.434  1.00  0.00           H  
HETATM   67  H24 UNL     1      -1.656  -4.781   0.046  1.00  0.00           H  
HETATM   68  H25 UNL     1      -4.299  -6.604  -0.296  1.00  0.00           H  
HETATM   69  H26 UNL     1       1.592  -3.363   2.887  1.00  0.00           H  
HETATM   70  H27 UNL     1       3.391  -3.206   2.712  1.00  0.00           H  
HETATM   71  H28 UNL     1       3.329  -4.217   0.502  1.00  0.00           H  
HETATM   72  H29 UNL     1       1.556  -4.540   0.616  1.00  0.00           H  
HETATM   73  H30 UNL     1       2.973  -7.774   1.646  1.00  0.00           H  
HETATM   74  H31 UNL     1       4.743  -2.335   1.583  1.00  0.00           H  
HETATM   75  H32 UNL     1       5.192  -0.749   0.881  1.00  0.00           H  
HETATM   76  H33 UNL     1       4.654  -0.883   2.676  1.00  0.00           H  
HETATM   77  H34 UNL     1       4.856   1.198   1.859  1.00  0.00           H  
CONECT    1    2    2   44   45
CONECT    2    3   46
CONECT    3    4    4   42
CONECT    4    5    6
CONECT    5   47   48   49
CONECT    6    7    7   41
CONECT    7    8   50
CONECT    8    9    9   39
CONECT    9   10
CONECT   10   11   11   33
CONECT   11   12   51
CONECT   12   13   27   27
CONECT   13   14   52
CONECT   14   15   25   25
CONECT   15   16   16   53
CONECT   16   17   22
CONECT   17   18   54
CONECT   18   19   19   20
CONECT   20   21   22   22
CONECT   21   55   56   57
CONECT   22   23
CONECT   23   24   24   58
CONECT   24   59   60
CONECT   25   26   27
CONECT   26   61   62   63
CONECT   27   28
CONECT   28   29   64   65
CONECT   29   30   66   67
CONECT   30   31   31   32
CONECT   32   68
CONECT   33   34   39   39
CONECT   34   35   69   70
CONECT   35   36   71   72
CONECT   36   37   37   38
CONECT   38   73
CONECT   39   40
CONECT   40   74   75   76
CONECT   41   42   77
CONECT   42   43   43
END
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SMILES for HMDB0001008 (Biliverdin)

CC1=C(C=C)\C(NC1=O)=C\C1=C(C)C(CCC(O)=O)=C(N1)\C=C1/N=C(/C=C2\NC(=O)C(C=C)=C2C)C(C)=C1CCC(O)=O
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INCHI for HMDB0001008 (Biliverdin)

InChI=1S/C33H34N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-15,35H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,28-15-
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View in JSmolView Stereo Labels
Synonyms
ValueSource
8,12-Bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbilin-1(19)(21H,24H)-dioneChEBI
Biliverdin IX alphaChEBI
Biliverdin ixalphaChEBI
BiliverdineChEBI
BILIVERDINE IX ALPHAChEBI
Biliverdin IX aGenerator
Biliverdin IX αGenerator
BILIVERDINE IX aGenerator
BILIVERDINE IX αGenerator
Biliverdin IXHMDB
1,3,6,7-Tetramethyl-4,5-dicarboxyethyl-2,8-divinylbilenoneHMDB
DehydrobilirubinHMDB
Protobiliverdin IXHMDB
UteroverdineHMDB
Chemical FormulaC33H34N4O6
Average Molecular Weight582.657
Monoisotopic Molecular Weight582.247834831
IUPAC Name3-(2-{[(2Z)-3-(2-carboxyethyl)-5-{[(2Z)-4-ethenyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-ylidene]methyl}-4-methyl-2H-pyrrol-2-ylidene]methyl}-5-{[(2Z)-3-ethenyl-4-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-ylidene]methyl}-4-methyl-1H-pyrrol-3-yl)propanoic acid
Traditional Namebiliverdine
CAS Registry Number114-25-0
SMILES
CC1=C(C=C)\C(NC1=O)=C\C1=C(C)C(CCC(O)=O)=C(N1)\C=C1/N=C(/C=C2\NC(=O)C(C=C)=C2C)C(C)=C1CCC(O)=O
InChI Identifier
InChI=1S/C33H34N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-15,35H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,28-15-
InChI KeyQBUVFDKTZJNUPP-BBROENKCSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as bilirubins. These are organic compounds containing a dicarboxylic acyclic tetrapyrrole derivative.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassBilirubins
Direct ParentBilirubins
Alternative Parents
Substituents
  • Bilirubin skeleton
  • Dipyrrin
  • Dicarboxylic acid or derivatives
  • Substituted pyrrole
  • Pyrrole
  • Pyrroline
  • Heteroaromatic compound
  • Carboxamide group
  • Ketimine
  • Lactam
  • Secondary carboxylic acid amide
  • Azacycle
  • Organic 1,3-dipolar compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Propargyl-type 1,3-dipolar organic compound
  • Hydrocarbon derivative
  • Imine
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic oxide
  • Organonitrogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Baker249.730932474
[M-H]-MetCCS_train_neg242.03930932474
[M+H]+Baker246.530932474
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane (predicted from logP)
  • Nucleus
Biospecimen Locations
  • Feces
Tissue Locations
  • Neuron
  • Placenta
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  3. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDDB02073
Phenol Explorer Compound IDNot Available
FooDB IDFDB022366
KNApSAcK IDNot Available
Chemspider ID10628548
KEGG Compound IDC00500
BioCyc IDBILIVERDINE
BiGG ID35167
Wikipedia LinkBiliverdin
METLIN ID5938
PubChem Compound5353439
PDB IDNot Available
ChEBI ID17033
Food Biomarker OntologyNot Available
VMH IDBILIVERD
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceMora, Maria E.; Bari, Sara E.; Awruch, Josefina; Delfino, Jose M. On how the conformation of biliverdins influences their reduction to bilirubins: A biological and molecular modeling study. Bioorganic & Medicinal Chemistry (2003), 11(21), 4661-467
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Briz O, Macias RI, Serrano MA, Gonzalez-Gallego J, Bayon JE, Marin JJ: Excretion of foetal bilirubin by the rat placenta-maternal liver tandem. Placenta. 2003 May;24(5):462-72. [PubMed:12744922 ]
  3. Trull FR, Ibars O, Lightner DA: Conformation inversion of bilirubin formed by reduction of the biliverdin-human serum albumin complex: evidence from circular dichroism. Arch Biochem Biophys. 1992 Nov 1;298(2):710-4. [PubMed:1416999 ]
  4. Kunikata T, Itoh S, Ozaki T, Kondo M, Isobe K, Onishi S: Formation of propentdyopents and biliverdin, oxidized metabolites of bilirubin, in infants receiving oxygen therapy. Pediatr Int. 2000 Aug;42(4):331-6. [PubMed:10986860 ]
  5. Odrcich MJ, Graham CH, Kimura KA, McLaughlin BE, Marks GS, Nakatsu K, Brien JF: Heme oxygenase and nitric oxide synthase in the placenta of the guinea-pig during gestation. Placenta. 1998 Sep;19(7):509-16. [PubMed:9778124 ]
  6. Poon HF, Calabrese V, Scapagnini G, Butterfield DA: Free radicals: key to brain aging and heme oxygenase as a cellular response to oxidative stress. J Gerontol A Biol Sci Med Sci. 2004 May;59(5):478-93. [PubMed:15123759 ]
  7. Beruter J, Colombo JP, Schlunegger UP: Isolation and identification of the urinary pigment uroerythrin. Eur J Biochem. 1975 Aug 1;56(1):239-44. [PubMed:1175621 ]
  8. Chrastil J: Spectrophotometric determination of cysteine and cystine in urine. Analyst. 1990 Oct;115(10):1383-4. [PubMed:2270876 ]
  9. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Enzymes

Enzyme Details
1. Heme oxygenase 2
General function:
Involved in heme oxygenase (decyclizing) activity
Specific function:
Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed. Heme oxygenase 2 could be implicated in the production of carbon monoxide in brain where it could act as a neurotransmitter.
Gene Name:
HMOX2
Uniprot ID:
P30519
Molecular weight:
36032.615
Reactions
Heme + AH(2) + Oxygen → Biliverdin + Fe2+ + CO + A + Waterdetails
Hemoglobin + FADH + Oxygen → Globin + Biliverdin + Carbon monoxide + Iron + FAD + Waterdetails
Enzyme Details
2. Heme oxygenase 1
General function:
Involved in heme oxygenase (decyclizing) activity
Specific function:
Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.
Gene Name:
HMOX1
Uniprot ID:
P09601
Molecular weight:
32818.345
Reactions
Heme + AH(2) + Oxygen → Biliverdin + Fe2+ + CO + A + Waterdetails
Hemoglobin + FADH + Oxygen → Globin + Biliverdin + Carbon monoxide + Iron + FAD + Waterdetails
Enzyme Details
3. Biliverdin reductase A
General function:
Involved in biliverdin reductase activity
Specific function:
Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.
Gene Name:
BLVRA
Uniprot ID:
P53004
Molecular weight:
33428.225
Reactions
Bilirubin + NAD(P)(+) → Biliverdin + NAD(P)Hdetails
Bilirubin + NAD → Biliverdin + NADH + Hydrogen Iondetails
Bilirubin + NADP → Biliverdin + NADPH + Hydrogen Iondetails
Enzyme Details
4. Flavin reductase (NADPH)
General function:
Involved in catalytic activity
Specific function:
Broad specificity oxidoreductase that catalyzes the NADPH-dependent reduction of a variety of flavins, such as riboflavin, FAD or FMN, biliverdins, methemoglobin and PQQ (pyrroloquinoline quinone). Contributes to heme catabolism and metabolizes linear tetrapyrroles. Can also reduce the complexed Fe(3+) iron to Fe(2+) in the presence of FMN and NADPH. In the liver, converts biliverdin to bilirubin.
Gene Name:
BLVRB
Uniprot ID:
P30043
Molecular weight:
22119.215
Reactions
Bilirubin + NAD(P)(+) → Biliverdin + NAD(P)Hdetails
Bilirubin + NAD → Biliverdin + NADH + Hydrogen Iondetails
Bilirubin + NADP → Biliverdin + NADPH + Hydrogen Iondetails
Enzyme Details
5. Aryl hydrocarbon receptor
General function:
Involved in transcription regulator activity
Specific function:
Ligand-activated transcriptional activator. Binds to the XRE promoter region of genes it activates. Activates the expression of multiple phase I and II xenobiotic chemical metabolizing enzyme genes (such as the CYP1A1 gene). Mediates biochemical and toxic effects of halogenated aromatic hydrocarbons. Involved in cell-cycle regulation. Likely to play an important role in the development and maturation of many tissues
Gene Name:
AHR
Uniprot ID:
P35869
Molecular weight:
96146.7