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Showing NP-Card for Homocysteine (NP0001013)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:20:07 UTC
NP-MRD IDNP0001013
Secondary Accession NumbersNone
Natural Product Identification
Common NameHomocysteine
DescriptionHomocysteine is a sulfur-containing amino acid that arises during methionine metabolism. Although its concentration in plasma is only about 10 micromolar (uM), even moderate hyperhomocysteinemia is associated with increased incidence of cardiovascular disease and Alzheimer's disease. Elevations in plasma homocysteine are commonly found as a result of vitamin deficiencies, polymorphisms of enzymes of methionine metabolism, and renal disease. Pyridoxal, folic acid, riboflavin, and Vitamin B(12) are all required for methionine metabolism, and deficiency of each of these vitamins result in elevated plasma homocysteine. A polymorphism of methylenetetrahydrofolate reductase (C677T), which is quite common in most populations with a homozygosity rate of 10-15 %, is associated with moderate hyperhomocysteinemia, especially in the context of marginal folate intake. Plasma homocysteine is inversely related to plasma creatinine in patients with renal disease. This is due to an impairment in homocysteine removal in renal disease. The role of these factors, and of modifiable lifestyle factors, in affecting methionine metabolism and in determining plasma homocysteine levels is discussed. Homocysteine is an independent cardiovascular disease (CVD) risk factor modifiable by nutrition and possibly exercise. Homocysteine was first identified as an important biological compound in 1932 and linked with human disease in 1962 when elevated urinary homocysteine levels were found in children with mental retardation. This condition, called homocysteinuria, was later associated with premature occlusive CVD, even in children. These observations led to research investigating the relationship of elevated homocysteine levels and CVD in a wide variety of populations including middle age and elderly men and women with and without traditional risk factors for CVD (PMID 17136938 , 15630149 ). Moreover, homocysteine is found to be associated with cystathionine beta-synthase deficiency, cystathioninuria, methylenetetrahydrofolate reductase deficiency, and sulfite oxidase deficiency, which are inborn errors of metabolism.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001013 (Homocysteine)


  Mrv1652309042000062D          

  8  7  0  0  0  0            999 V2000
 9993.2233 9993.3504    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9993.9374 9993.7625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.6531 9993.3504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.3686 9993.7625    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5086 9993.7625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.7936 9993.3504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5086 9994.5873    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.2233 9992.5250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  8  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
Download

3D MOL for NP0001013 (Homocysteine)

HMDB0000742
     RDKit          3D
Homocysteine
 17 16  0  0  0  0  0  0  0  0999 V2000
    0.0389   -0.1354    1.2899 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5221    0.0125   -0.0315 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2992    0.8858   -0.9225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7117    0.3946   -1.1000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5223    0.3373    0.5280 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.8951    0.5930    0.0296 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4922    0.7992   -1.0446 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5185    0.9062    1.2345 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3396   -1.0469    1.5473 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5317    0.3877    2.0261 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6503   -1.0110   -0.4723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3395    1.9007   -0.4888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2154    0.9723   -1.8995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2542    1.1458   -1.7144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7630   -0.5965   -1.5832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6891   -1.0248    0.8884 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0543    0.1761    1.7129 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
Download

3D SDF for NP0001013 (Homocysteine)


  Mrv1652309042000062D          

  8  7  0  0  0  0            999 V2000
 9993.2233 9993.3504    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9993.9374 9993.7625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.6531 9993.3504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.3686 9993.7625    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5086 9993.7625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.7936 9993.3504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5086 9994.5873    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.2233 9992.5250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  8  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0001013

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1

> <INCHI_KEY>
FFFHZYDWPBMWHY-VKHMYHEASA-N

> <FORMULA>
C4H9NO2S

> <MOLECULAR_WEIGHT>
135.185

> <EXACT_MASS>
135.035399227

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.536000221060835

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.29

> <JCHEM_LOGP>
-2.5764673824810185

> <ALOGPS_LOGS>
-0.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.279400411474743

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.458553724459435

> <JCHEM_PKA_STRONGEST_BASIC>
9.413365429707895

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
32.934999999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.48e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-homocysteine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001013 (Homocysteine)

HMDB0000742
     RDKit          3D
Homocysteine
 17 16  0  0  0  0  0  0  0  0999 V2000
    0.0389   -0.1354    1.2899 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5221    0.0125   -0.0315 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2992    0.8858   -0.9225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7117    0.3946   -1.1000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5223    0.3373    0.5280 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.8951    0.5930    0.0296 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4922    0.7992   -1.0446 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5185    0.9062    1.2345 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3396   -1.0469    1.5473 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5317    0.3877    2.0261 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6503   -1.0110   -0.4723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3395    1.9007   -0.4888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2154    0.9723   -1.8995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2542    1.1458   -1.7144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7630   -0.5965   -1.5832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6891   -1.0248    0.8884 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0543    0.1761    1.7129 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 NP0001013 (Homocysteine)

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    8654.0178654.254   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8655.3508655.023   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8656.6868654.254   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0    8658.0218655.023   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0    8652.6838655.023   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8651.3488654.254   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8652.6838656.563   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0    8654.0178652.713   0.000  0.00  0.00           N+0
CONECT    1    2    5    8                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    1    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    1                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for NP0001013 (Homocysteine)

COMPND    HMDB0000742
HETATM    1  N1  UNL     1       0.039  -0.135   1.290  1.00  0.00           N  
HETATM    2  C1  UNL     1       0.522   0.012  -0.031  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.299   0.886  -0.922  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.712   0.395  -1.100  1.00  0.00           C  
HETATM    5  S1  UNL     1      -2.522   0.337   0.528  1.00  0.00           S  
HETATM    6  C4  UNL     1       1.895   0.593   0.030  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.492   0.799  -1.045  1.00  0.00           O  
HETATM    8  O2  UNL     1       2.519   0.906   1.235  1.00  0.00           O  
HETATM    9  H1  UNL     1      -0.340  -1.047   1.547  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.532   0.388   2.026  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.650  -1.011  -0.472  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.339   1.901  -0.489  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.215   0.972  -1.900  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.254   1.146  -1.714  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.763  -0.597  -1.583  1.00  0.00           H  
HETATM   16  H8  UNL     1      -2.689  -1.025   0.888  1.00  0.00           H  
HETATM   17  H9  UNL     1       3.054   0.176   1.713  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 NP0001013 (Homocysteine)

N[C@@H](CCS)C(O)=O
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INCHI for NP0001013 (Homocysteine)

InChI=1S/C4H9NO2S/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 JSmol
Synonyms
ValueSource
HcyChEBI
L-2-Amino-4-mercaptobutyric acidChEBI
L-2-Amino-4-mercaptobutyrateGenerator
2-Amino-4-mercaptobutyric acidHMDB
Homocysteine, L isomerHMDB
L-Isomer homocysteineHMDB
2 Amino 4 mercaptobutyric acidHMDB
Homocysteine, L-isomerHMDB
(S)-2-Amino-4-mercapto-butanoateHMDB
(S)-2-Amino-4-mercapto-butanoic acidHMDB
(S)-2-Amino-4-mercaptobutanoic acidHMDB
(S)-HomocysteineHMDB
2-Amino-4-mercapto-DL-butyrateHMDB
2-Amino-4-mercapto-DL-butyric acidHMDB
2-Amino-4-mercapto-L-butyric acidHMDB
2-Amino-4-mercapto-butanoateHMDB
2-Amino-4-mercapto-butanoic acidHMDB
2-Amino-4-mercapto-butyric acidHMDB
2-Amino-4-sulfanylbutanoateHMDB
2-Amino-4-sulfanylbutanoic acidHMDB
D,L-HomocysteineHMDB
DL-2-Amino-4-mercapto-butyric acidHMDB
DL-2-Amino-4-mercaptobutyric acidHMDB
DL-HomocysteineHMDB
Homo-cysHMDB
L-2-Amino-4-mercapto-butyric acidHMDB
L-HomocysteineHMDB
2-Amino-4-mercapto-butyrateHMDB
HomocysteineMeSH, KEGG
Chemical FormulaC4H9NO2S
Average Mass135.1850 Da
Monoisotopic Mass135.03540 Da
IUPAC Name(2S)-2-amino-4-sulfanylbutanoic acid
Traditional NameL-homocysteine
CAS Registry Number454-29-5
SMILES
N[C@@H](CCS)C(O)=O
InChI Identifier
InChI=1S/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m0/s1
InChI KeyFFFHZYDWPBMWHY-VKHMYHEASA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaKNApSAcK Database
Cannabis sativaCannabisDB
      Not Available
Homo sapiensLOTUS Database
Mus musculusLOTUS Database
Spinacia oleraceaKNApSAcK Database
Species Where Detected
Species NameSourceReference
Escherichia coliKNApSAcK Database
Homo sapiens (Urine)KNApSAcK Database
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
  • Thia fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Alkylthiol
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point232 - 233 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility148 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility14.8 g/LALOGPS
logP-2.3ALOGPS
logP-2.6ChemAxon
logS-0.96ALOGPS
pKa (Strongest Acidic)2.46ChemAxon
pKa (Strongest Basic)9.41ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity32.94 m³·mol⁻¹ChemAxon
Polarizability13.54 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000742
DrugBank IDDB04422
Phenol Explorer Compound IDNot Available
FoodDB IDFDB112371
KNApSAcK IDC00001365
Chemspider ID82666
KEGG Compound IDC00155
BioCyc IDHOMO-CYS
BiGG IDNot Available
Wikipedia LinkHomocysteine
METLIN ID3256
PubChem Compound91552
PDB IDNot Available
ChEBI ID17588
Good Scents IDNot Available
References
General References
  1. Selley ML, Close DR, Stern SE: The effect of increased concentrations of homocysteine on the concentration of (E)-4-hydroxy-2-nonenal in the plasma and cerebrospinal fluid of patients with Alzheimer's disease. Neurobiol Aging. 2002 May-Jun;23(3):383-8. [PubMed:11959400 ]
  2. Yu CK, Lakasing L, Papageorghiou AT, Spencer K, Nicolaides KH: Uterine artery Doppler and mid-trimester maternal plasma homocysteine in subsequent pre-eclampsia. J Matern Fetal Neonatal Med. 2004 Aug;16(2):134-9. [PubMed:15512726 ]
  3. Giladi N, Mordechovich M, Gruendlinger L, Shabtai H, Merims D, Naor S, Baltadzhieva R, Hausdorff JM, Gur AY, Bornstein NM: "Brain Screen": A self-referral, screening program for strokes, falls and dementia risk factors. J Neurol. 2006 Mar;253(3):307-15. Epub 2005 Oct 10. [PubMed:16208527 ]
  4. Terzolo M, Allasino B, Bosio S, Brusa E, Daffara F, Ventura M, Aroasio E, Sacchetto G, Reimondo G, Angeli A, Camaschella C: Hyperhomocysteinemia in patients with Cushing's syndrome. J Clin Endocrinol Metab. 2004 Aug;89(8):3745-51. [PubMed:15292300 ]
  5. Laxdal E, Eide GE, Amundsen SR, Dregelid EB, Pedersen G, Jonung T, Aune S: Homocysteine levels, haemostatic risk factors and restenosis after carotid thrombendarterectomy. Eur J Vasc Endovasc Surg. 2004 Sep;28(3):323-8. [PubMed:15288638 ]
  6. Akoglu B, Wondra K, Caspary WF, Faust D: Determinants of fasting total serum homocysteine levels in liver transplant recipients. Exp Clin Transplant. 2006 Jun;4(1):462-6. [PubMed:16827644 ]
  7. Krantz JS, Mack WJ, Hodis HN, Liu CR, Liu CH, Kaufman FR: Early onset of subclinical atherosclerosis in young persons with type 1 diabetes. J Pediatr. 2004 Oct;145(4):452-7. [PubMed:15480366 ]
  8. Serot JM, Barbe F, Arning E, Bottiglieri T, Franck P, Montagne P, Nicolas JP: Homocysteine and methylmalonic acid concentrations in cerebrospinal fluid: relation with age and Alzheimer's disease. J Neurol Neurosurg Psychiatry. 2005 Nov;76(11):1585-7. [PubMed:16227558 ]
  9. Hershcovici T, Schechner V, Orlin J, Harell D, Beigel Y: Effect of different LDL-apheresis methods on parameters involved in atherosclerosis. J Clin Apher. 2004;19(2):90-7. [PubMed:15274202 ]
  10. Muller T, Renger K, Kuhn W: Levodopa-associated increase of homocysteine levels and sural axonal neurodegeneration. Arch Neurol. 2004 May;61(5):657-60. [PubMed:15148140 ]
  11. Eskes TK: Homocysteine and human reproduction. Clin Exp Obstet Gynecol. 2000;27(3-4):157-67. [PubMed:11214939 ]
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