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Showing NP-Card for D-Cysteine (NP0000745)

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Record Information
Version2.0
Created at2006-08-12 20:29:18 UTC
Updated at2021-08-19 23:58:25 UTC
NP-MRD IDNP0000745
Secondary Accession NumbersNone
Natural Product 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 NP0000745 (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 NP0000745 (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 NP0000745 (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>
NP0000745

> <DATABASE_NAME>
NP-MRD

> <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 NP0000745 (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 NP0000745 (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 NP0000745 (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 NP0000745 (D-Cysteine)

N[C@H](CS)C(O)=O
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INCHI for NP0000745 (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 JSmol
Synonyms
ValueSource
(2S)-2-Amino-3-mercaptopropanoic acidChEBI
(2S)-2-Amino-3-sulfanylpropanoic acidChEBI
(S)-2-Amino-3-mercaptopropanoic acidChEBI
D-Amino-3-mercaptopropionic acidChEBI
D-CysteinChEBI
D-ZysteinChEBI
DCYChEBI
(2S)-2-Amino-3-mercaptopropanoateGenerator
(2S)-2-Amino-3-sulfanylpropanoateGenerator
(2S)-2-Amino-3-sulphanylpropanoateGenerator
(2S)-2-Amino-3-sulphanylpropanoic acidGenerator
(S)-2-Amino-3-mercaptopropanoateGenerator
D-Amino-3-mercaptopropionateGenerator
CysteineHMDB
Half cystineHMDB
Cysteine hydrochlorideHMDB
Half-cystineHMDB
L-CysteineHMDB
L CysteineHMDB
Zinc cysteinateHMDB
Chemical FormulaC3H7NO2S
Average Mass121.1500 Da
Monoisotopic Mass121.01975 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)Varshavi.d262021-08-31View 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
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-08-03View Spectrum
Species
Species of Origin
Species NameSourceReference
Allium cepaLOTUS Database
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Arabidopsis thalianaKNApSAcK Database
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Cucurbita foetidissimaLOTUS Database
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Gossypium hirsutumLOTUS Database
Homo sapiensLOTUS Database
Indigofera hendecaphyllaLOTUS Database
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Nicotiana tabacumLOTUS Database
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
Pentaclethra macrophyllaLOTUS Database
PhasianidaeFooDB
Phasianus colchicusFooDB
Pisum sativumLOTUS Database
Prunus domesticaLOTUS Database
Ripariosida hermaphroditaLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Telekia speciosaLOTUS Database
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
Physical Properties
StateSolid
Experimental 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
Predicted Properties
PropertyValueSource
Water Solubility23.1 g/LALOGPS
logP-2.6ALOGPS
logP-2.8ChemAxon
logS-0.72ALOGPS
pKa (Strongest Acidic)2.35ChemAxon
pKa (Strongest Basic)9.05ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity28.22 m³·mol⁻¹ChemAxon
Polarizability11.4 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0003417
DrugBank IDDB03201
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDrw1353141
References
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 ]
  3. Shibuya N, Koike S, Tanaka M, Ishigami-Yuasa M, Kimura Y, Ogasawara Y, Fukui K, Nagahara N, Kimura H: A novel pathway for the production of hydrogen sulfide from D-cysteine in mammalian cells. Nat Commun. 2013;4:1366. doi: 10.1038/ncomms2371. [PubMed:23340406 ]
  4. Kimura H: Signaling molecules: hydrogen sulfide and polysulfide. Antioxid Redox Signal. 2015 Feb 10;22(5):362-76. doi: 10.1089/ars.2014.5869. Epub 2014 Jun 25. [PubMed:24800864 ]