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Showing NP-Card for D-Methionine (NP0002744)

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Record Information
Version2.0
Created at2020-11-23 19:39:21 UTC
Updated at2024-09-17 15:45:36 UTC
NP-MRD IDNP0002744
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Methionine
Provided ByBMRBBMRB logo
DescriptionD-Methionine is also known as MED. D-Methionine is found in Allium cepa, Allium sativum, Artemia salina, Astragalus hamosus, Brassica napus, Calendula officinalis, Cucumaria frondosa, Daphnia pulex, Flammulina velutipes, Glycine max, Gossypium hirsutum, Indigofera schimperi, Jatropha gossypiifolia, Juncus roemerianus, Morchella angusticeps, Nicotiana tabacum, Opuntia ficus-indica, Panax ginseng, Pentaclethra macrophylla, Phyllostachys nigra, Pinus contorta, Pinus densiflora, Pinus ponderosa, Pisum sativum, Prunus domestica, Psophocarpus tetragonolobus, Sida hermaphrodita, Senna obtusifolia, Spermacoce pusilla, Suaeda aegyptiaca and Tacca cristata. D-Methionine was first documented in 2010 (PMID: 20431016). Based on a literature review a small amount of articles have been published on D-Methionine (PMID: 20872028) (PMID: 21480759).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002744 (D-Methionine)


  Mrv1652303202019002D          

  9  8  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for NP0002744 (D-Methionine)

NP0002744
     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
    3.4312   -0.6219   -0.0395 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6363    0.7873    0.7553 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9770    1.0255    0.0298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1477   -0.1740    0.4169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2539   -0.1339   -0.1077 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9033   -1.3570    0.3572 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0533    1.0092    0.3193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7634    2.2160    0.0737 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2189    0.8159    1.0454 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9314   -1.3004    0.6870 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1339   -0.2288   -0.8035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6607   -1.2307   -0.5603 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5400    1.9773    0.3324 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1078    1.0520   -1.0676 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0989   -0.3131    1.5086 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6251   -1.0863   -0.0108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2325   -0.1834   -1.2260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8470   -1.4909   -0.0524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9031   -1.3680    1.4087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1147    0.6054    0.6228 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
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  6
  6 18  1  0
  6 19  1  0
  9 20  1  0
M  END
Download

3D SDF for NP0002744 (D-Methionine)


  Mrv1652303202019002D          

  9  8  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0002744

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1

> <INCHI_KEY>
FFEARJCKVFRZRR-SCSAIBSYSA-N

> <FORMULA>
C5H11NO2S

> <MOLECULAR_WEIGHT>
149.211

> <EXACT_MASS>
149.051049291

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
15.464914492672031

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-4-(methylsulfanyl)butanoic acid

> <ALOGPS_LOGP>
-1.85

> <JCHEM_LOGP>
-2.189326616871282

> <ALOGPS_LOGS>
-0.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5319210041042344

> <JCHEM_PKA_STRONGEST_BASIC>
9.502323343916569

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
37.586000000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.39e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-methionine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002744 (D-Methionine)

NP0002744
     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
    3.4312   -0.6219   -0.0395 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6363    0.7873    0.7553 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9770    1.0255    0.0298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1477   -0.1740    0.4169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2539   -0.1339   -0.1077 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9033   -1.3570    0.3572 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0533    1.0092    0.3193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7634    2.2160    0.0737 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2189    0.8159    1.0454 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9314   -1.3004    0.6870 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1339   -0.2288   -0.8035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6607   -1.2307   -0.5603 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5400    1.9773    0.3324 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1078    1.0520   -1.0676 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0989   -0.3131    1.5086 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6251   -1.0863   -0.0108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2325   -0.1834   -1.2260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8470   -1.4909   -0.0524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9031   -1.3680    1.4087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1147    0.6054    0.6228 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
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  6
  6 18  1  0
  6 19  1  0
  9 20  1  0
M  END
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PDB for NP0002744 (D-Methionine)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       4.620   2.667   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       8.621   4.977   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for NP0002744 (D-Methionine)

COMPND    NP0002744
HETATM    1  C1  UNL     1       3.431  -0.622  -0.040  1.00  0.00           C  
HETATM    2  S1  UNL     1       2.636   0.787   0.755  1.00  0.00           S  
HETATM    3  C2  UNL     1       0.977   1.026   0.030  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.148  -0.174   0.417  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.254  -0.134  -0.108  1.00  0.00           C  
HETATM    6  N1  UNL     1      -1.903  -1.357   0.357  1.00  0.00           N  
HETATM    7  C5  UNL     1      -2.053   1.009   0.319  1.00  0.00           C  
HETATM    8  O1  UNL     1      -1.763   2.216   0.074  1.00  0.00           O  
HETATM    9  O2  UNL     1      -3.219   0.816   1.045  1.00  0.00           O  
HETATM   10  H1  UNL     1       3.931  -1.300   0.687  1.00  0.00           H  
HETATM   11  H2  UNL     1       4.134  -0.229  -0.803  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.661  -1.231  -0.560  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.540   1.977   0.332  1.00  0.00           H  
HETATM   14  H5  UNL     1       1.108   1.052  -1.068  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.099  -0.313   1.509  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.625  -1.086  -0.011  1.00  0.00           H  
HETATM   17  H8  UNL     1      -1.232  -0.183  -1.226  1.00  0.00           H  
HETATM   18  H9  UNL     1      -2.847  -1.491  -0.052  1.00  0.00           H  
HETATM   19  H10 UNL     1      -1.903  -1.368   1.409  1.00  0.00           H  
HETATM   20  H11 UNL     1      -4.115   0.605   0.623  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3
CONECT    3    4   13   14
CONECT    4    5   15   16
CONECT    5    6    7   17
CONECT    6   18   19
CONECT    7    8    8    9
CONECT    9   20
END
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SMILES for NP0002744 (D-Methionine)

CSCC[C@@H](N)C(O)=O
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INCHI for NP0002744 (D-Methionine)

InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1
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View in JSmolView NMR Assignments
Synonyms
ValueSource
(2R)-2-Amino-4-(methylsulfanyl)butanoic acidChEBI
(R)-2-Amino-4-(methylthio)butanoic acidChEBI
(R)-MethionineChEBI
D-2-Amino-4-(methylthio)butyric acidChEBI
D-MethioninChEBI
MEDChEBI
(2R)-2-Amino-4-(methylsulfanyl)butanoateGenerator
(2R)-2-Amino-4-(methylsulphanyl)butanoateGenerator
(2R)-2-Amino-4-(methylsulphanyl)butanoic acidGenerator
(R)-2-Amino-4-(methylthio)butanoateGenerator
D-2-Amino-4-(methylthio)butyrateGenerator
L-Isomer methionineMeSH
L-MethionineMeSH
PedamethMeSH
LiquimethMeSH
Methionine, L isomerMeSH
Methionine, L-isomerMeSH
MethionineMeSH
Chemical FormulaC5H11NO2S
Average Mass149.2110 Da
Monoisotopic Mass149.05105 Da
IUPAC Name(2R)-2-amino-4-(methylsulfanyl)butanoic acid
Traditional NameD-methionine
CAS Registry NumberNot Available
SMILES
CSCC[C@@H](N)C(O)=O
InChI Identifier
InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1
InChI KeyFFEARJCKVFRZRR-SCSAIBSYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Allium cepaLOTUS Database
Allium sativumLOTUS Database
Artemia salinaLOTUS Database
Astragalus hamosusLOTUS Database
Brassica napusLOTUS Database
Calendula officinalisLOTUS Database
Cannabis sativaCannabisDB
      Not Available
Cucumaria frondosaLOTUS Database
Daphnia pulexLOTUS Database
Flammulina velutipesLOTUS Database
Glycine maxLOTUS Database
Gossypium hirsutumLOTUS Database
Indigofera schimperiLOTUS Database
Jatropha gossypifoliaLOTUS Database
Juncus roemerianusLOTUS Database
Morchella angusticepsLOTUS Database
Nicotiana tabacumLOTUS Database
Opuntia ficus-indicaLOTUS Database
Panax ginsengLOTUS Database
Pentaclethra macrophyllaLOTUS Database
Phyllostachys nigraLOTUS Database
Pinus contortaLOTUS Database
Pinus densifloraLOTUS Database
Pinus ponderosaLOTUS Database
Pisum sativumLOTUS Database
Prunus domesticaLOTUS Database
Psophocarpus tetragonolobusLOTUS Database
Ripariosida hermaphroditaLOTUS Database
Senna obtusifoliaLOTUS Database
Spermacoce pusillaLOTUS Database
Suaeda aegyptiacaLOTUS Database
Tacca cristataLOTUS Database
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as methionine and derivatives. These are compounds containing methionine or a derivative thereof resulting from reaction of methionine 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 ParentMethionine and derivatives
Alternative Parents
Substituents
  • Methionine or derivatives
  • Alpha-amino acid
  • D-alpha-amino acid
  • Thia fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Thioether
  • Sulfenyl compound
  • Dialkylthioether
  • Amine
  • Organic oxygen compound
  • Primary amine
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting Point273.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Boiling Point306.90 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility25740 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP0.370 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
logP-1.8ALOGPS
logP-2.2ChemAxon
logS-0.8ALOGPS
pKa (Strongest Acidic)2.53ChemAxon
pKa (Strongest Basic)9.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity37.59 m³·mol⁻¹ChemAxon
Polarizability15.46 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDDB02893
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID76512
KEGG Compound IDC00855
BioCyc IDCPD-218
BiGG IDNot Available
Wikipedia LinkMethionine
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID16867
Good Scents IDrw1108051
References
General References
  1. Kolodkin-Gal I, Romero D, Cao S, Clardy J, Kolter R, Losick R: D-amino acids trigger biofilm disassembly. Science. 2010 Apr 30;328(5978):627-9. doi: 10.1126/science.1188628. [PubMed:20431016 ]
  2. Hasegawa H, Shinohara Y, Akahane K, Hashimoto T, Ichida K: Altered D: -methionine kinetics in rats with renal impairment. Amino Acids. 2011 Apr;40(4):1205-11. doi: 10.1007/s00726-010-0746-5. Epub 2010 Sep 25. [PubMed:20872028 ]
  3. Alagic Z, Goiny M, Canlon B: Protection against acoustic trauma by direct application of D-methionine to the inner ear. Acta Otolaryngol. 2011 Aug;131(8):802-8. doi: 10.3109/00016489.2011.564652. Epub 2011 Apr 11. [PubMed:21480759 ]