Showing metabocard for D-Cysteine (MMDBc0000243)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:41:05 UTC
Update Date2024-10-11 03:58:24 UTC
Metabolite IDMMDBc0000243
Metabolite Identification
Common NameD-Cysteine
DescriptionD-Cysteine is a naturally occurring enantiomer of L-Cysteine. It is a non-proteogenic sulfur-containing amino acid. Cysteine is named after cystine, which comes from the Greek word kustis meaning bladder − cystine was first isolated from kidney stones. (wikipedia) D-cysteine can be generated from L-cysteine via cysteine racemase. D-Cysteine is known to be toxic to bacteria and several bacteria (and plants) have developed and enzyme called D-cysteine desulfhydrase (EC 4.1.99.4). This enzyme decomposes D-cysteine into pyruvate, H2S, and NH3. (PMID: 15720402 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645c9f2f6d8>


  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 #<Metabolite:0x00005645c9f2f6d8>

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 #<Metabolite:0x00005645c9f2f6d8>


  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>
MMDBc0000243

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00005645c9f2f6d8>

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 #<Metabolite:0x00005645c9f2f6d8>

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 #<Metabolite:0x00005645c9f2f6d8>

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 #<Metabolite:0x00005645c9f2f6d8>

N[C@H](CS)C(O)=O
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INCHI for #<Metabolite:0x00005645c9f2f6d8>

InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1
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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
CysteineMeSH, HMDB
Half cystineMeSH, HMDB
Cysteine hydrochlorideMeSH, HMDB
Half-cystineMeSH, HMDB
L-CysteineMeSH, HMDB
L CysteineMeSH, HMDB
Zinc cysteinateMeSH, HMDB
Molecular FormulaC3H7NO2S
Average Mass121.15
Monoisotopic Mass121.019749643
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