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Showing metabocard for Homogentisic acid (HMDB0000130)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:32 UTC
HMDB IDHMDB0000130
Secondary Accession Numbers
  • HMDB00130
Metabolite Identification
Common NameHomogentisic acid
Description
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000130 (Homogentisic acid)

  Mrv1652309032023532D          

 12 12  0  0  0  0            999 V2000
10000.356310000.8239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.071110000.4119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.783810000.8239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.0711 9999.5890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.931710001.6478    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9317 9998.3521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.644810000.4128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.930410000.8253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.215810000.4127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2158 9999.5878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9303 9999.1753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6448 9999.5878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12  7  1  0  0  0  0
 11  6  1  0  0  0  0
  8  5  1  0  0  0  0
  1  7  1  0  0  0  0
M  END
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3D MOL for HMDB0000130 (Homogentisic acid)

HMDB0000130
     RDKit          3D
Homogentisic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.8418    1.0101    1.3869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5931    0.0744    0.5704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5253   -0.0766   -0.4638 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4064   -0.7398    0.7663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1341   -0.2087    0.2983 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9465   -1.0864    0.3148 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1825   -0.6978   -0.1585 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2838   -1.5365   -0.1591 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3217    0.5907   -0.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2516    1.4225   -0.6535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0067    1.0677   -0.1865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0433    1.9503   -0.2186 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2683   -0.7417   -1.1794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3209   -0.9291    1.8641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5618   -1.7175    0.2129 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8805   -2.1186    0.7038 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1258   -2.4908    0.2179 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3124    0.9201   -1.0227 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3953    2.4325   -1.0515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9984    2.8751   -0.5918 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11  5  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  6 16  1  0
  8 17  1  0
  9 18  1  0
 10 19  1  0
 12 20  1  0
M  END
Download

3D SDF for HMDB0000130 (Homogentisic acid)

  Mrv1652309032023532D          

 12 12  0  0  0  0            999 V2000
10000.356310000.8239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.071110000.4119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.783810000.8239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.0711 9999.5890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.931710001.6478    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9317 9998.3521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.644810000.4128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.930410000.8253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.215810000.4127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2158 9999.5878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9303 9999.1753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6448 9999.5878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12  7  1  0  0  0  0
 11  6  1  0  0  0  0
  8  5  1  0  0  0  0
  1  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000130

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CC1=C(O)C=CC(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C8H8O4/c9-6-1-2-7(10)5(3-6)4-8(11)12/h1-3,9-10H,4H2,(H,11,12)

> <INCHI_KEY>
IGMNYECMUMZDDF-UHFFFAOYSA-N

> <FORMULA>
C8H8O4

> <MOLECULAR_WEIGHT>
168.1467

> <EXACT_MASS>
168.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
15.568374170369944

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(2,5-dihydroxyphenyl)acetic acid

> <ALOGPS_LOGP>
0.81

> <JCHEM_LOGP>
1.0038634619999998

> <ALOGPS_LOGS>
-1.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.566007893833087

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.57380421430248

> <JCHEM_PKA_STRONGEST_BASIC>
-5.895788377591718

> <JCHEM_POLAR_SURFACE_AREA>
77.75999999999999

> <JCHEM_REFRACTIVITY>
41.3274

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.10e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
homogentisic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000130 (Homogentisic acid)

HMDB0000130
     RDKit          3D
Homogentisic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.8418    1.0101    1.3869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5931    0.0744    0.5704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5253   -0.0766   -0.4638 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4064   -0.7398    0.7663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1341   -0.2087    0.2983 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9465   -1.0864    0.3148 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1825   -0.6978   -0.1585 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2838   -1.5365   -0.1591 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3217    0.5907   -0.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2516    1.4225   -0.6535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0067    1.0677   -0.1865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0433    1.9503   -0.2186 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2683   -0.7417   -1.1794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3209   -0.9291    1.8641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5618   -1.7175    0.2129 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8805   -2.1186    0.7038 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1258   -2.4908    0.2179 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3124    0.9201   -1.0227 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3953    2.4325   -1.0515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9984    2.8751   -0.5918 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11  5  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  6 16  1  0
  8 17  1  0
  9 18  1  0
 10 19  1  0
 12 20  1  0
M  END
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PDB for HMDB0000130 (Homogentisic acid)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0    8667.3328668.205   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8668.6668667.436   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8669.9968668.205   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8668.6668665.899   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8664.6738669.743   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8664.6738663.591   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8666.0048667.437   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8664.6708668.207   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8663.3368667.437   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8663.3368665.897   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8664.6708665.127   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8666.0048665.897   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    8                                                            
CONECT    6   11                                                            
CONECT    7    8   12    1                                                  
CONECT    8    7    9    5                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12    6                                                  
CONECT   12   11    7                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for HMDB0000130 (Homogentisic acid)

COMPND    HMDB0000130
HETATM    1  O1  UNL     1      -2.842   1.010   1.387  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.593   0.074   0.570  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.525  -0.077  -0.464  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.406  -0.740   0.766  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.134  -0.209   0.298  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.946  -1.086   0.315  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.183  -0.698  -0.158  1.00  0.00           C  
HETATM    8  O3  UNL     1       3.284  -1.536  -0.159  1.00  0.00           O  
HETATM    9  C6  UNL     1       2.322   0.591  -0.650  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.252   1.423  -0.653  1.00  0.00           C  
HETATM   11  C8  UNL     1      -0.007   1.068  -0.186  1.00  0.00           C  
HETATM   12  O4  UNL     1      -1.043   1.950  -0.219  1.00  0.00           O  
HETATM   13  H1  UNL     1      -3.268  -0.742  -1.179  1.00  0.00           H  
HETATM   14  H2  UNL     1      -1.321  -0.929   1.864  1.00  0.00           H  
HETATM   15  H3  UNL     1      -1.562  -1.718   0.213  1.00  0.00           H  
HETATM   16  H4  UNL     1       0.881  -2.119   0.704  1.00  0.00           H  
HETATM   17  H5  UNL     1       3.126  -2.491   0.218  1.00  0.00           H  
HETATM   18  H6  UNL     1       3.312   0.920  -1.023  1.00  0.00           H  
HETATM   19  H7  UNL     1       1.395   2.432  -1.051  1.00  0.00           H  
HETATM   20  H8  UNL     1      -0.998   2.875  -0.592  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   13
CONECT    4    5   14   15
CONECT    5    6    6   11
CONECT    6    7   16
CONECT    7    8    9    9
CONECT    8   17
CONECT    9   10   18
CONECT   10   11   11   19
CONECT   11   12
CONECT   12   20
END
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SMILES for HMDB0000130 (Homogentisic acid)

OC(=O)CC1=C(O)C=CC(O)=C1
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INCHI for HMDB0000130 (Homogentisic acid)

InChI=1S/C8H8O4/c9-6-1-2-7(10)5(3-6)4-8(11)12/h1-3,9-10H,4H2,(H,11,12)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC8H8O4
Average Molecular Weight168.1467
Monoisotopic Molecular Weight168.042258744
IUPAC Name2-(2,5-dihydroxyphenyl)acetic acid
Traditional Namehomogentisic acid
CAS Registry Number451-13-8
SMILES
OC(=O)CC1=C(O)C=CC(O)=C1
InChI Identifier
InChI=1S/C8H8O4/c9-6-1-2-7(10)5(3-6)4-8(11)12/h1-3,9-10H,4H2,(H,11,12)
InChI KeyIGMNYECMUMZDDF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 2(hydroxyphenyl)acetic acids. These are phenylacetic acids that carry a hydroxyl group at the 2-position.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassPhenylacetic acids
Direct Parent2(hydroxyphenyl)acetic acids
Alternative Parents
Substituents
  • 2(hydroxyphenyl)acetic acid
  • Hydroquinone
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point153 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility850 mg/mL at 25 °CNot Available
LogP0.86SANGSTER (1994)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available133.1http://allccs.zhulab.cn/database/detail?ID=AllCCS00000526
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Cartilage
  • Kidney
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Crohn's disease
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Ulcerative colitis
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Alkaptonuria
  1. Phornphutkul C, Introne WJ, Perry MB, Bernardini I, Murphey MD, Fitzpatrick DL, Anderson PD, Huizing M, Anikster Y, Gerber LH, Gahl WA: Natural history of alkaptonuria. N Engl J Med. 2002 Dec 26;347(26):2111-21. [PubMed:12501223 ]
  2. La Du BN Jr: Are we ready to try to cure alkaptonuria? Am J Hum Genet. 1998 Apr;62(4):765-7. [PubMed:9529368 ]
  3. Bory C, Boulieu R, Chantin C, Mathieu M: Diagnosis of alcaptonuria: rapid analysis of homogentisic acid by HPLC. Clin Chim Acta. 1990 Jul;189(1):7-11. [PubMed:2383921 ]
  4. Datta AK, Mandal S, Dasgupta A, Ghosh TK: Alkaptonuria diagnosed in a 4-month-old baby girl: a case report. Cases J. 2008 Nov 13;1(1):308. doi: 10.1186/1757-1626-1-308. [PubMed:19014543 ]
  5. Olah AV, Llyes I, Szoke A, Csizy I, Toth J, Varga J: Urinary homogentisic acid in alkaptonuric and healthy children. Clin Chem Lab Med. 2003 Mar;41(3):356-9. [PubMed:12705346 ]
  6. Thalagahage KN, Jayaweera JA, Kumbukgolla WW, Senavirathne I: Detection of alkaptonuria in a 1-week-old infant. BMJ Case Rep. 2015 May 8;2015. pii: bcr2014208505. doi: 10.1136/bcr-2014-208505. [PubMed:25956497 ]
  7. Bory C, Boulieu R, Chantin C, Mathieu M: Homogentisic acid determined in biological fluids by HPLC. Clin Chem. 1989 Feb;35(2):321-2. [PubMed:2914385 ]
  8. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDDB08327
Phenol Explorer Compound IDNot Available
FooDB IDFDB030907
KNApSAcK IDC00007309
Chemspider ID759
KEGG Compound IDC00544
BioCyc IDHOMOGENTISATE
BiGG ID1485308
Wikipedia LinkHomogentisic_acid
METLIN ID331
PubChem Compound780
PDB IDNot Available
ChEBI ID44747
Food Biomarker OntologyNot Available
VMH IDHGENTIS
MarkerDB IDMDB00000062
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. 4-hydroxyphenylpyruvate dioxygenase
General function:
Involved in 4-hydroxyphenylpyruvate dioxygenase activity
Specific function:
Key enzyme in the degradation of tyrosine.
Gene Name:
HPD
Uniprot ID:
P32754
Molecular weight:
40497.105
Reactions
4-Hydroxyphenylpyruvic acid + Oxygen → Homogentisic acid + CO(2)details
4-Hydroxyphenylpyruvic acid + Oxygen → Homogentisic acid + Carbon dioxidedetails
Enzyme Details
2. Homogentisate 1,2-dioxygenase
General function:
Involved in homogentisate 1,2-dioxygenase activity
Specific function:
Not Available
Gene Name:
HGD
Uniprot ID:
Q93099
Molecular weight:
49963.41
Reactions
Homogentisic acid + Oxygen → Maleylacetoacetic aciddetails