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Showing metabocard for Selenohomocysteine (HMDB0004119)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-08-13 11:34:05 UTC
Update Date2023-02-21 17:16:56 UTC
HMDB IDHMDB0004119
Secondary Accession Numbers
  • HMDB04119
Metabolite Identification
Common NameSelenohomocysteine
DescriptionSelenohomocysteine (CAS: 29412-93-9) is the precursor of selenocysteine, which is synthesized by the catalysis of cystathionine beta-synthase (EC 4.2.1.22) and cystathionine gamma-lyase (EC 4.4.1.1) in mammalian systems (both enzymes require pyridoxal phosphate). Selenohomocysteine (lactone) has been found to be a competitive and irreversible inhibitor of lysyl oxidase; this may relate to the development of connective tissue defects seen in homocystinuria. L-Selenohomocysteine also can serve as a substituent donor in the beta-replacement reaction to yield selenocystathionine (PMID: 10609891 , 9405445 , 6456763 , 3338973 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0004119 (Selenohomocysteine)

 
  Mrv1652309042000302D          

  8  7  0  0  1  0            999 V2000
   31.2511  -25.1991    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   31.9622  -24.7808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.4982  -24.7808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.2511  -26.0357    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   32.6733  -25.1991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.7871  -25.1991    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.4982  -23.9442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   33.4262  -24.7808    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  2  0  0  0  0
  5  8  1  0  0  0  0
M  END
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3D MOL for HMDB0004119 (Selenohomocysteine)

HMDB0004119
     RDKit          3D
Selenohomocysteine
 17 16  0  0  0  0  0  0  0  0999 V2000
    1.0953   -1.1548    0.5970 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5990   -0.5663   -0.5751 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8887   -0.7366   -0.7462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6740   -0.1240    0.3833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3960    1.7575    0.5898 Se  0  0  0  0  0  2  0  0  0  0  0  0
    1.0145    0.8511   -0.7153 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6906    1.5753   -1.6801 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8069    1.3918    0.2871 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0309   -1.5705    0.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6948   -0.9152    1.4869 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0663   -1.1011   -1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1022   -1.8244   -0.7432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2044   -0.3410   -1.7194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7584   -0.2854    0.1276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5123   -0.6389    1.3422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2616    2.1290    2.0724 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7994    1.5535    0.1755 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  6
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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3D SDF for HMDB0004119 (Selenohomocysteine)

 
  Mrv1652309042000302D          

  8  7  0  0  1  0            999 V2000
   31.2511  -25.1991    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   31.9622  -24.7808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.4982  -24.7808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.2511  -26.0357    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   32.6733  -25.1991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.7871  -25.1991    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.4982  -23.9442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   33.4262  -24.7808    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  2  0  0  0  0
  5  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0004119

> <DATABASE_NAME>
hmdb

> <SMILES>
N[C@@H](CC[SeH])C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO2Se/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1

> <INCHI_KEY>
RCWCGLALNCIQNM-VKHMYHEASA-N

> <FORMULA>
C4H9NO2Se

> <MOLECULAR_WEIGHT>
182.092

> <EXACT_MASS>
182.979851

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.663330212350402

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-4-selanylbutanoic acid

> <ALOGPS_LOGP>
-3.07

> <JCHEM_LOGP>
-3.8710500043959426

> <ALOGPS_LOGS>
0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.279399840528317

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.407390701390531

> <JCHEM_PKA_STRONGEST_BASIC>
9.413362639466056

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
38.158300000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.10e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-amino-4-selanylbutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0004119 (Selenohomocysteine)

HMDB0004119
     RDKit          3D
Selenohomocysteine
 17 16  0  0  0  0  0  0  0  0999 V2000
    1.0953   -1.1548    0.5970 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5990   -0.5663   -0.5751 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8887   -0.7366   -0.7462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6740   -0.1240    0.3833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3960    1.7575    0.5898 Se  0  0  0  0  0  2  0  0  0  0  0  0
    1.0145    0.8511   -0.7153 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6906    1.5753   -1.6801 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8069    1.3918    0.2871 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0309   -1.5705    0.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6948   -0.9152    1.4869 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0663   -1.1011   -1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1022   -1.8244   -0.7432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2044   -0.3410   -1.7194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7584   -0.2854    0.1276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5123   -0.6389    1.3422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2616    2.1290    2.0724 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7994    1.5535    0.1755 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  6
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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PDB for HMDB0004119 (Selenohomocysteine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      58.335 -47.038   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      59.663 -46.257   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      56.930 -46.257   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      58.335 -48.600   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      60.990 -47.038   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      55.603 -47.038   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      56.930 -44.696   0.000  0.00  0.00           O+0
HETATM    8 Se   UNK     0      62.396 -46.257   0.000  0.00  0.00          Se+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6    7                                                  
CONECT    4    1                                                            
CONECT    5    2    8                                                       
CONECT    6    3                                                            
CONECT    7    3                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0004119 (Selenohomocysteine)

COMPND    HMDB0004119
HETATM    1  N1  UNL     1       1.095  -1.155   0.597  1.00  0.00           N  
HETATM    2  C1  UNL     1       0.599  -0.566  -0.575  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.889  -0.737  -0.746  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.674  -0.124   0.383  1.00  0.00           C  
HETATM    5 SE1  UNL     1      -1.396   1.758   0.590  1.00  0.00          SE  
HETATM    6  C4  UNL     1       1.015   0.851  -0.715  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.691   1.575  -1.680  1.00  0.00           O  
HETATM    8  O2  UNL     1       1.807   1.392   0.287  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.031  -1.571   0.572  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.695  -0.915   1.487  1.00  0.00           H  
HETATM   11  H3  UNL     1       1.066  -1.101  -1.455  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.102  -1.824  -0.743  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.204  -0.341  -1.719  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.758  -0.285   0.128  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.512  -0.639   1.342  1.00  0.00           H  
HETATM   16  H8  UNL     1      -1.262   2.129   2.072  1.00  0.00           H  
HETATM   17  H9  UNL     1       2.799   1.554   0.176  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3    6   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5   16
CONECT    6    7    7    8
CONECT    8   17
END
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SMILES for HMDB0004119 (Selenohomocysteine)

N[C@@H](CC[SeH])C(O)=O
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INCHI for HMDB0004119 (Selenohomocysteine)

InChI=1S/C4H9NO2Se/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Seleno-L-homocysteineChEBI
(2S)-2-Amino-4-selanylbutanoic acidHMDB
(2S)-2-Amino-4-selenylbutanoic acidHMDB
2-Amino-4-selenobutanoic acidHMDB
L-SelenohomocysteineHMDB
SelenohomocysteineChEBI
Chemical FormulaC4H9NO2Se
Average Molecular Weight182.092
Monoisotopic Molecular Weight182.979851
IUPAC Name(2S)-2-amino-4-selanylbutanoic acid
Traditional Name(2S)-2-amino-4-selanylbutanoic acid
CAS Registry Number29475-60-3
SMILES
N[C@@H](CC[SeH])C(O)=O
InChI Identifier
InChI=1S/C4H9NO2Se/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1
InChI KeyRCWCGLALNCIQNM-VKHMYHEASA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Fatty acid
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Selenol
  • Primary amine
  • Organoselenium compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Route of exposureSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023315
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC05698
BioCyc IDSELENOHOMOCYSTEINE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound49787004
PDB IDNot Available
ChEBI ID9096
Food Biomarker OntologyNot Available
VMH IDSELHCYS
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Esaki N, Nakamura T, Tanaka H, Suzuki T, Morino Y, Soda K: Enzymatic synthesis of selenocysteine in rat liver. Biochemistry. 1981 Jul 21;20(15):4492-6. [PubMed:6456763 ]
  2. Soda K, Oikawa T, Esaki N: Vitamin B6 enzymes participating in selenium amino acid metabolism. Biofactors. 1999;10(2-3):257-62. [PubMed:10609891 ]
  3. Liu G, Nellaiappan K, Kagan HM: Irreversible inhibition of lysyl oxidase by homocysteine thiolactone and its selenium and oxygen analogues. Implications for homocystinuria. J Biol Chem. 1997 Dec 19;272(51):32370-7. [PubMed:9405445 ]
  4. Esaki N, Seraneeprakarn V, Tanaka H, Soda K: Purification and characterization of Clostridium sticklandii D-selenocystine alpha, beta-lyase. J Bacteriol. 1988 Feb;170(2):751-6. [PubMed:3338973 ]

Enzymes

Enzyme Details
1. Methionine synthase
General function:
Involved in cobalamin binding
Specific function:
Catalyzes the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate (By similarity).
Gene Name:
MTR
Uniprot ID:
Q99707
Molecular weight:
140525.91
Reactions
Selenohomocysteine + 5-Methyltetrahydropteroyltri-L-glutamic acid → Selenomethionine + Tetrahydropteroyltri-L-glutamic aciddetails
Enzyme Details
2. Putative adenosylhomocysteinase 3
General function:
Involved in adenosylhomocysteinase activity
Specific function:
Not Available
Gene Name:
AHCYL2
Uniprot ID:
Q96HN2
Molecular weight:
66592.445
Reactions
Se-Adenosylselenohomocysteine + Water → Adenosine + Selenohomocysteinedetails
Enzyme Details
3. Adenosylhomocysteinase
General function:
Involved in adenosylhomocysteinase activity
Specific function:
Adenosylhomocysteine is a competitive inhibitor of S-adenosyl-L-methionine-dependent methyl transferase reactions; therefore adenosylhomocysteinase may play a key role in the control of methylations via regulation of the intracellular concentration of adenosylhomocysteine.
Gene Name:
AHCY
Uniprot ID:
P23526
Molecular weight:
47715.715
Reactions
Se-Adenosylselenohomocysteine + Water → Adenosine + Selenohomocysteinedetails
Enzyme Details
4. Putative adenosylhomocysteinase 2
General function:
Involved in adenosylhomocysteinase activity
Specific function:
Not Available
Gene Name:
AHCYL1
Uniprot ID:
O43865
Molecular weight:
53753.0
Reactions
Se-Adenosylselenohomocysteine + Water → Adenosine + Selenohomocysteinedetails
Enzyme Details
5. Cystathionine beta-synthase
General function:
Involved in cysteine biosynthetic process from serine
Specific function:
Only known pyridoxal phosphate-dependent enzyme that contains heme. Important regulator of hydrogen sulfide, especially in the brain, utilizing cysteine instead of serine to catalyze the formation of hydrogen sulfide. Hydrogen sulfide is a gastratransmitter with signaling and cytoprotective effects such as acting as a neuromodulator in the brain to protect neurons against hypoxic injury (By similarity).
Gene Name:
CBS
Uniprot ID:
P35520
Molecular weight:
60586.05
Reactions
Serine + Selenohomocysteine → Selenocystathionine + Waterdetails