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Showing metabocard for D-Cysteine (HMDB0003417)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-12 20:29:18 UTC
Update Date2021-10-13 04:41:39 UTC
HMDB IDHMDB0003417
Secondary Accession Numbers
  • HMDB03417
Metabolite Identification
Common NameD-Cysteine
DescriptionD-cysteine is an optically active form of cysteine having D-configuration. It is a cysteine and a D-alpha-amino acid. It is a conjugate base of a D-cysteinium. It is a conjugate acid of a D-cysteinate(1-). It is an enantiomer of a L-cysteine. It is a tautomer of a D-cysteine zwitterion. D-Cysteine, also known as D-cystein or DCY, belongs to the class of organic compounds known as cysteine and derivatives. Cysteine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. It is a non-proteogenic sulfur-containing amino acid. D-Cysteine is known to be toxic to bacteria and several bacteria (and plants) have developed and enzyme called D-cysteine desulfhydrase (EC4.1.99.4). D-cysteine can be generated from D-Cysteine via cysteine racemase. D-Cysteine is a naturally occurring enantiomer of L-Cysteine. Cysteine is named after cystine, which comes from the Greek word kustis meaning bladder -cystine was first isolated from kidney stones. D-Cysteine exists in all living species, ranging from bacteria to humans. Outside of the human body, D-Cysteine has been detected, but not quantified in several different foods, such as chervils, fruits, lichee, nuts, and cherimoya.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003417 (D-Cysteine)

  Mrv1652305271900072D          

  7  6  0  0  1  0            999 V2000
    0.6124    0.2357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1021   -0.1768    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8165    0.2357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3269   -0.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6124    1.0607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1021   -1.0018    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5310   -0.1768    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  5  1  2  0  0  0  0
  4  1  1  0  0  0  0
  3  2  1  0  0  0  0
  2  6  1  6  0  0  0
  7  3  1  0  0  0  0
M  END
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3D MOL for HMDB0003417 (D-Cysteine)

HMDB0003417
     RDKit          3D
D-Cysteine
 14 13  0  0  0  0  0  0  0  0999 V2000
    0.3079    1.6533   -0.2733 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3223    0.5046    0.2970 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6467   -0.5646    0.7381 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6563   -1.2032   -0.5870 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3411   -0.0363   -0.6379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5335    0.5260   -1.7525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1041   -1.1537   -0.3326 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1415    1.6381   -1.3025 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3439    1.6952   -0.0813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8571    0.8413    1.2283 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2127   -0.2238    1.6283 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0065   -1.4160    1.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9532   -0.6617   -0.6087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1106   -1.5992    0.5676 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
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  1
  3 11  1  0
  3 12  1  0
  4 13  1  0
  7 14  1  0
M  END
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3D SDF for HMDB0003417 (D-Cysteine)

  Mrv1652305271900072D          

  7  6  0  0  1  0            999 V2000
    0.6124    0.2357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1021   -0.1768    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8165    0.2357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3269   -0.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6124    1.0607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1021   -1.0018    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5310   -0.1768    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  5  1  2  0  0  0  0
  4  1  1  0  0  0  0
  3  2  1  0  0  0  0
  2  6  1  6  0  0  0
  7  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003417

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1

> <INCHI_KEY>
XUJNEKJLAYXESH-UWTATZPHSA-N

> <FORMULA>
C3H7NO2S

> <MOLECULAR_WEIGHT>
121.15

> <EXACT_MASS>
121.019749643

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
11.401989924934824

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-3-sulfanylpropanoic acid

> <ALOGPS_LOGP>
-2.57

> <JCHEM_LOGP>
-2.7921332976482773

> <ALOGPS_LOGS>
-0.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.171891903949282

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.345995198078135

> <JCHEM_PKA_STRONGEST_BASIC>
9.053809511128133

> <JCHEM_POLAR_SURFACE_AREA>
63.31999999999999

> <JCHEM_REFRACTIVITY>
28.2236

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.31e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L cysteine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0003417 (D-Cysteine)

HMDB0003417
     RDKit          3D
D-Cysteine
 14 13  0  0  0  0  0  0  0  0999 V2000
    0.3079    1.6533   -0.2733 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3223    0.5046    0.2970 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6467   -0.5646    0.7381 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6563   -1.2032   -0.5870 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3411   -0.0363   -0.6379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5335    0.5260   -1.7525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1041   -1.1537   -0.3326 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1415    1.6381   -1.3025 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3439    1.6952   -0.0813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8571    0.8413    1.2283 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2127   -0.2238    1.6283 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0065   -1.4160    1.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9532   -0.6617   -0.6087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1106   -1.5992    0.5676 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
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  1
  3 11  1  0
  3 12  1  0
  4 13  1  0
  7 14  1  0
M  END
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PDB for HMDB0003417 (D-Cysteine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       1.143   0.440   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.191  -0.330   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.524   0.440   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.477  -0.330   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       1.143   1.980   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      -0.191  -1.870   0.000  0.00  0.00           N+0
HETATM    7  S   UNK     0      -2.858  -0.330   0.000  0.00  0.00           S+0
CONECT    1    2    5    4                                                  
CONECT    2    1    3    6                                                  
CONECT    3    2    7                                                       
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2                                                            
CONECT    7    3                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0003417 (D-Cysteine)

COMPND    HMDB0003417
HETATM    1  N1  UNL     1       0.308   1.653  -0.273  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.322   0.505   0.297  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.647  -0.565   0.738  1.00  0.00           C  
HETATM    4  S1  UNL     1       1.656  -1.203  -0.587  1.00  0.00           S  
HETATM    5  C3  UNL     1      -1.341  -0.036  -0.638  1.00  0.00           C  
HETATM    6  O1  UNL     1      -1.533   0.526  -1.752  1.00  0.00           O  
HETATM    7  O2  UNL     1      -2.104  -1.154  -0.333  1.00  0.00           O  
HETATM    8  H1  UNL     1       0.142   1.638  -1.302  1.00  0.00           H  
HETATM    9  H2  UNL     1       1.344   1.695  -0.081  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.857   0.841   1.228  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.213  -0.224   1.628  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.006  -1.416   1.117  1.00  0.00           H  
HETATM   13  H6  UNL     1       2.953  -0.662  -0.609  1.00  0.00           H  
HETATM   14  H7  UNL     1      -2.111  -1.599   0.568  1.00  0.00           H  
CONECT    1    2    8    9
CONECT    2    3    5   10
CONECT    3    4   11   12
CONECT    4   13
CONECT    5    6    6    7
CONECT    7   14
END
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SMILES for HMDB0003417 (D-Cysteine)

N[C@H](CS)C(O)=O
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INCHI for HMDB0003417 (D-Cysteine)

InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC3H7NO2S
Average Molecular Weight121.15
Monoisotopic Molecular Weight121.019749643
IUPAC Name(2S)-2-amino-3-sulfanylpropanoic acid
Traditional NameL cysteine
CAS Registry Number921-01-7
SMILES
N[C@H](CS)C(O)=O
InChI Identifier
InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1
InChI KeyXUJNEKJLAYXESH-UWTATZPHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cysteine and derivatives. Cysteine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentCysteine and derivatives
Alternative Parents
Substituents
  • Cysteine or derivatives
  • Alpha-amino acid
  • D-alpha-amino acid
  • Amino acid
  • Alkylthiol
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic oxygen compound
  • Primary amine
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point293.90 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility113200 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP0.230 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected and Quantified8.643 +/- 2.11 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03201
Phenol Explorer Compound IDNot Available
FooDB IDFDB023168
KNApSAcK IDC00007323
Chemspider ID83819
KEGG Compound IDC00793
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCysteine
METLIN IDNot Available
PubChem Compound92851
PDB IDNot Available
ChEBI ID16375
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1353141
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Tsukamoto S, Kanegae T, Nagoya T, Shimamura M, Mieda Y, Nomura M, Hojo K, Okubo H: Effects of amino acids on acute alcohol intoxication in mice--concentrations of ethanol, acetaldehyde, acetate and acetone in blood and tissues. Arukoru Kenkyuto Yakubutsu Ison. 1990 Oct;25(5):429-40. [PubMed:2275637 ]
  2. Riemenschneider A, Wegele R, Schmidt A, Papenbrock J: Isolation and characterization of a D-cysteine desulfhydrase protein from Arabidopsis thaliana. FEBS J. 2005 Mar;272(5):1291-304. [PubMed:15720402 ]