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Showing NP-Card for DL-Homocysteine (NP0002738)

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Record Information
Version1.0
Created at2020-11-23 19:39:12 UTC
Updated at2021-08-12 19:52:00 UTC
NP-MRD IDNP0002738
Secondary Accession NumbersNone
Natural Product Identification
Common NameDL-Homocysteine
Provided ByBMRBBMRB logo
Description It was first documented in 2008 (PMID: 17984079). Based on a literature review very few articles have been published on (2R)-2-amino-4-sulfanylbutanoic acid.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002738 (DL-Homocysteine)


     RDKit          2D

 17 16  0  0  0  0  0  0  0  0999 V2000
    0.2404   -2.0288    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9825   -0.7252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3211    0.0169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6247    0.7590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9282    1.5011    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7246    0.5784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1301    1.9555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2246    0.5875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9983   -3.3232    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2473   -2.2207    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2861   -1.4673    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2566    1.4012    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2165   -1.1865    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3667   -0.5446    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8826    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2227    0.7432    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9666    1.8910    0.0000 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  1
  3 12  1  1
  3 13  1  0
  4 14  1  1
  4 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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3D MOL for NP0002738 (DL-Homocysteine)

NP0002738
     RDKit          3D

 17 16  0  0  0  0  0  0  0  0999 V2000
   -0.8410   -1.8120    0.0424 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9075   -0.5063   -0.5366 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4567    0.0681   -0.8304 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3078    0.2007    0.4031 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9102    0.9065   -0.1368 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7622    0.4047    0.2382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3115   -0.0497    1.2748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9988    1.7098   -0.0926 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0915   -2.1307    0.3220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5564   -1.9170    0.8036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4062   -0.6268   -1.5434 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9682   -0.6491   -1.5060 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3560    1.0143   -1.3525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9051    0.8766    1.1569 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5461   -0.7917    0.8372 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7437    1.1551    0.9888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5017    2.1475   -0.8644 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 NP0002738 (DL-Homocysteine)


     RDKit          2D

 17 16  0  0  0  0  0  0  0  0999 V2000
    0.2404   -2.0288    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9825   -0.7252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3211    0.0169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6247    0.7590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9282    1.5011    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7246    0.5784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1301    1.9555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2246    0.5875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9983   -3.3232    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2473   -2.2207    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2861   -1.4673    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2566    1.4012    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2165   -1.1865    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3667   -0.5446    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8826    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2227    0.7432    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9666    1.8910    0.0000 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  1
  3 12  1  1
  3 13  1  0
  4 14  1  1
  4 15  1  0
  5 16  1  0
  8 17  1  0
M  END
> <DATABASE_ID>
NP0002738

> <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-/m1/s1

> <INCHI_KEY>
FFFHZYDWPBMWHY-GSVOUGTGSA-N

> <FORMULA>
C4H9NO2S

> <MOLECULAR_WEIGHT>
135.18

> <EXACT_MASS>
135.035399708

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.53931147467802

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.5764673824810185

> <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>
63.32000000000001

> <JCHEM_REFRACTIVITY>
32.935

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(+-)-homocysteine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002738 (DL-Homocysteine)

NP0002738
     RDKit          3D

 17 16  0  0  0  0  0  0  0  0999 V2000
   -0.8410   -1.8120    0.0424 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9075   -0.5063   -0.5366 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4567    0.0681   -0.8304 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3078    0.2007    0.4031 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9102    0.9065   -0.1368 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7622    0.4047    0.2382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3115   -0.0497    1.2748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9988    1.7098   -0.0926 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0915   -2.1307    0.3220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5564   -1.9170    0.8036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4062   -0.6268   -1.5434 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9682   -0.6491   -1.5060 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3560    1.0143   -1.3525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9051    0.8766    1.1569 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5461   -0.7917    0.8372 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7437    1.1551    0.9888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5017    2.1475   -0.8644 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

PDB for NP0002738 (DL-Homocysteine)

HEADER    PROTEIN                                 23-NOV-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-NOV-20         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
HETATM    8  S   UNK     0      -0.357   1.334   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    8                                                       
CONECT    3    1    4    5                                                  
CONECT    4    3    6    7                                                  
CONECT    5    3                                                            
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    2                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for NP0002738 (DL-Homocysteine)

COMPND    NP0002738
HETATM    1  N1  UNL     1      -0.841  -1.812   0.042  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.908  -0.506  -0.537  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.457   0.068  -0.830  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.308   0.201   0.403  1.00  0.00           C  
HETATM    5  S1  UNL     1       2.910   0.906  -0.137  1.00  0.00           S  
HETATM    6  C4  UNL     1      -1.762   0.405   0.238  1.00  0.00           C  
HETATM    7  O1  UNL     1      -2.312  -0.050   1.275  1.00  0.00           O  
HETATM    8  O2  UNL     1      -1.999   1.710  -0.093  1.00  0.00           O  
HETATM    9  H1  UNL     1       0.092  -2.131   0.322  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.556  -1.917   0.804  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.406  -0.627  -1.543  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.968  -0.649  -1.506  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.356   1.014  -1.353  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.905   0.877   1.157  1.00  0.00           H  
HETATM   15  H7  UNL     1       1.546  -0.792   0.837  1.00  0.00           H  
HETATM   16  H8  UNL     1       3.744   1.155   0.989  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.502   2.147  -0.864  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 NP0002738 (DL-Homocysteine)

N[C@H](CCS)C(O)=O
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INCHI for NP0002738 (DL-Homocysteine)

InChI=1S/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)/t3-/m1/s1
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View in JSmol
Synonyms
ValueSource
(2R)-2-Amino-4-sulfanylbutanoateGenerator
(2R)-2-Amino-4-sulphanylbutanoateGenerator
(2R)-2-Amino-4-sulphanylbutanoic acidGenerator
Chemical FormulaC4H9NO2S
Average Mass135.1800 Da
Monoisotopic Mass135.03540 Da
IUPAC Name(2R)-2-amino-4-sulfanylbutanoic acid
Traditional Name(+-)-homocysteine
CAS Registry NumberNot Available
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-/m1/s1
InChI KeyFFFHZYDWPBMWHY-GSVOUGTGSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.6ChemAxon
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 IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID118632
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]