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Showing NP-Card for N-Methyl-D-aspartic acid (NP0000151)

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Record Information
Version2.0
Created at2006-05-22 14:17:51 UTC
Updated at2021-08-19 20:22:35 UTC
NP-MRD IDNP0000151
Secondary Accession NumbersNone
Natural Product Identification
Common NameN-Methyl-D-aspartic acid
DescriptionN-Methyl-D-aspartic acid is an amino acid derivative acting as a specific agonist at the NMDA receptor, and therefore mimics the action of the neurotransmitter glutamate on that receptor. In contrast to glutamate, NMDA binds to and regulates the above receptor only, but not other glutamate receptors. NMDA is a water-soluble endogenous metabolite that plays an important role in the neuroendocrine system of species across Animalia (PMID: 18096065 ). It was first synthesized in the 1960s (PMID: 14056452 ). NMDA is an excitotoxin; this trait has applications in behavioural neuroscience research. The body of work utilizing this technique falls under the term "lesion studies." Researchers apply NMDA to specific regions of an (animal) subject's brain or spinal cord and subsequently test for the behaviour of interest, such as operant behaviour. If the behaviour is compromised, it suggests that the destroyed tissue was part of a brain region that made an important contribution to the normal expression of that behaviour. Examples of antagonists of the NMDA receptor are ketamine, amantadine, dextromethorphan (DXM), riluzole, and memantine. They are commonly referred to as NMDA receptor antagonists (PMID: 28877137 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000151 (N-Methyl-D-aspartic acid)


  Mrv1652305271900232D          

 10  9  0  0  1  0            999 V2000
   24.8397  -15.6908    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.2672  -15.2783    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.1251  -14.4533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.9817  -16.5158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.4107  -16.5158    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.4107  -15.6908    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.6962  -15.2783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.6962  -16.9283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1251  -15.2783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.9817  -15.6908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
  3  9  2  0  0  0  0
  4 10  2  0  0  0  0
  6  5  1  6  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
M  END
Download

3D MOL for NP0000151 (N-Methyl-D-aspartic acid)

HMDB0002393
     RDKit          3D
N-Methyl-D-aspartic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.2195   -0.5874   -0.2799 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1253   -0.2153   -1.0356 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1120    0.2315   -0.4822 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7257   -0.9175    0.3471 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0529   -0.5889    0.8619 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4036   -0.7793    1.9747 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9500   -0.0699   -0.0420 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1644    1.3832    0.4470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3265    1.4113    1.6236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2080    2.6322   -0.2651 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1366   -0.4880   -0.9399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4047    0.0850    0.5698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2301   -1.6762    0.0077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9218   -0.9073   -1.8266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8229    0.5123   -1.2008 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7891   -1.7832   -0.3350 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0602   -1.1829    1.2395 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8802    0.2383    0.2052 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0597    2.7021   -0.8695 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  2  0
  5  7  1  0
  3  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  3 15  1  6
  4 16  1  0
  4 17  1  0
  7 18  1  0
 10 19  1  0
M  END
Download

3D SDF for NP0000151 (N-Methyl-D-aspartic acid)


  Mrv1652305271900232D          

 10  9  0  0  1  0            999 V2000
   24.8397  -15.6908    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.2672  -15.2783    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.1251  -14.4533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.9817  -16.5158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.4107  -16.5158    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.4107  -15.6908    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.6962  -15.2783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.6962  -16.9283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1251  -15.2783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.9817  -15.6908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
  3  9  2  0  0  0  0
  4 10  2  0  0  0  0
  6  5  1  6  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000151

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN[C@H](CC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO4/c1-6-3(5(9)10)2-4(7)8/h3,6H,2H2,1H3,(H,7,8)(H,9,10)/t3-/m1/s1

> <INCHI_KEY>
HOKKHZGPKSLGJE-GSVOUGTGSA-N

> <FORMULA>
C5H9NO4

> <MOLECULAR_WEIGHT>
147.1293

> <EXACT_MASS>
147.053157781

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
13.175055068911252

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-(methylamino)butanedioic acid

> <ALOGPS_LOGP>
-2.58

> <JCHEM_LOGP>
-3.2736424766128556

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.999787472023925

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4571202479278589

> <JCHEM_PKA_STRONGEST_BASIC>
10.33837281139982

> <JCHEM_POLAR_SURFACE_AREA>
86.63

> <JCHEM_REFRACTIVITY>
31.307299999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N methyl D aspartate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000151 (N-Methyl-D-aspartic acid)

HMDB0002393
     RDKit          3D
N-Methyl-D-aspartic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.2195   -0.5874   -0.2799 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1253   -0.2153   -1.0356 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1120    0.2315   -0.4822 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7257   -0.9175    0.3471 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0529   -0.5889    0.8619 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4036   -0.7793    1.9747 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9500   -0.0699   -0.0420 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1644    1.3832    0.4470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3265    1.4113    1.6236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2080    2.6322   -0.2651 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1366   -0.4880   -0.9399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4047    0.0850    0.5698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2301   -1.6762    0.0077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9218   -0.9073   -1.8266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8229    0.5123   -1.2008 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7891   -1.7832   -0.3350 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0602   -1.1829    1.2395 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8802    0.2383    0.2052 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0597    2.7021   -0.8695 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  2  0
  5  7  1  0
  3  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  3 15  1  6
  4 16  1  0
  4 17  1  0
  7 18  1  0
 10 19  1  0
M  END
Download

PDB for NP0000151 (N-Methyl-D-aspartic acid)

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  O   UNK     0      46.367 -29.289   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      39.699 -28.519   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      45.034 -26.979   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      41.033 -30.829   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      43.700 -30.829   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      43.700 -29.289   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      42.366 -28.519   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      42.366 -31.599   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      45.034 -28.519   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      41.033 -29.289   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3    9                                                            
CONECT    4   10                                                            
CONECT    5    6    8                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6   10                                                       
CONECT    8    5                                                            
CONECT    9    1    3    6                                                  
CONECT   10    2    4    7                                                  
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for NP0000151 (N-Methyl-D-aspartic acid)

COMPND    HMDB0002393
HETATM    1  C1  UNL     1      -2.219  -0.587  -0.280  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.125  -0.215  -1.036  1.00  0.00           N  
HETATM    3  C2  UNL     1       0.112   0.232  -0.482  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.726  -0.917   0.347  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.053  -0.589   0.862  1.00  0.00           C  
HETATM    6  O1  UNL     1       2.404  -0.779   1.975  1.00  0.00           O  
HETATM    7  O2  UNL     1       2.950  -0.070  -0.042  1.00  0.00           O  
HETATM    8  C5  UNL     1      -0.164   1.383   0.447  1.00  0.00           C  
HETATM    9  O3  UNL     1      -0.327   1.411   1.624  1.00  0.00           O  
HETATM   10  O4  UNL     1      -0.208   2.632  -0.265  1.00  0.00           O  
HETATM   11  H1  UNL     1      -3.137  -0.488  -0.940  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.405   0.085   0.570  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.230  -1.676   0.008  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.922  -0.907  -1.827  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.823   0.512  -1.201  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.789  -1.783  -0.335  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.060  -1.183   1.239  1.00  0.00           H  
HETATM   18  H8  UNL     1       3.880   0.238   0.205  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.060   2.702  -0.870  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3   14
CONECT    3    4    8   15
CONECT    4    5   16   17
CONECT    5    6    6    7
CONECT    7   18
CONECT    8    9    9   10
CONECT   10   19
END
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SMILES for NP0000151 (N-Methyl-D-aspartic acid)

CN[C@H](CC(O)=O)C(O)=O
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INCHI for NP0000151 (N-Methyl-D-aspartic acid)

InChI=1S/C5H9NO4/c1-6-3(5(9)10)2-4(7)8/h3,6H,2H2,1H3,(H,7,8)(H,9,10)/t3-/m1/s1
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View in JSmol
Synonyms
ValueSource
(R)-2-Methylamino-succinic acidChEBI
2-Methylamino-succinic acidChEBI
Methyl aspartic acidChEBI
N-Methyl aspartic acidChEBI
N-Methyl-D-aspartateChEBI
N-MethylaspartateChEBI
NMDAChEBI
(R)-2-Methylamino-succinateGenerator
2-Methylamino-succinateGenerator
Methyl aspartateGenerator
N-Methyl aspartateGenerator
N-Methylaspartic acidGenerator
N-Me-D-asp-OHHMDB
N-Methyl D-aspartateHMDB
N-Methyl D-aspartic acidHMDB
N Methyl D aspartateHMDB
N Methyl D aspartic acidHMDB
Acid, N-methyl-D-asparticHMDB
N MethylaspartateHMDB
Chemical FormulaC5H9NO4
Average Mass147.1293 Da
Monoisotopic Mass147.05316 Da
IUPAC Name(2R)-2-(methylamino)butanedioic acid
Traditional NameN methyl D aspartate
CAS Registry Number6384-92-5
SMILES
CN[C@H](CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H9NO4/c1-6-3(5(9)10)2-4(7)8/h3,6H,2H2,1H3,(H,7,8)(H,9,10)/t3-/m1/s1
InChI KeyHOKKHZGPKSLGJE-GSVOUGTGSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)V.dorna832021-08-29View 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)varshavi.d26@gmail.comNot AvailableNot Available2021-07-25View Spectrum
Species
Species of Origin
Species NameSourceReference
Bos taurusMilk
Chemical Taxonomy
Description Belongs to the class of organic compounds known as aspartic acid and derivatives. Aspartic acid and derivatives are compounds containing an aspartic acid or a derivative thereof resulting from reaction of aspartic acid 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 ParentAspartic acid and derivatives
Alternative Parents
Substituents
  • Aspartic acid or derivatives
  • Alpha-amino acid
  • D-alpha-amino acid
  • Dicarboxylic acid or derivatives
  • Fatty acid
  • Amino acid
  • Carboxylic acid
  • Secondary aliphatic amine
  • Secondary amine
  • Amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point187 - 192 °CNot Available
Boiling Point258.24 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.390 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility40.6 g/LALOGPS
logP-2.6ALOGPS
logP-3.3ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)1.46ChemAxon
pKa (Strongest Basic)10.34ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.63 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.31 m³·mol⁻¹ChemAxon
Polarizability13.18 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002393
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022992
KNApSAcK IDNot Available
Chemspider ID21436
KEGG Compound IDC12269
BioCyc IDCPD-10705
BiGG IDNot Available
Wikipedia LinkN-Methyl-D-aspartic_acid
METLIN ID6662
PubChem Compound22880
PDB IDNot Available
ChEBI ID31882
Good Scents IDrw1359131
References
General References
  1. Baskys A, Fang L, Bayazitov I: Activation of neuroprotective pathways by metabotropic group I glutamate receptors: a potential target for drug discovery? Ann N Y Acad Sci. 2005 Aug;1053:55-73. [PubMed:16179509 ]
  2. Hitchcock IS, Skerry TM, Howard MR, Genever PG: NMDA receptor-mediated regulation of human megakaryocytopoiesis. Blood. 2003 Aug 15;102(4):1254-9. Epub 2003 Mar 20. [PubMed:12649130 ]
  3. Miller RF: D-Serine as a glial modulator of nerve cells. Glia. 2004 Aug 15;47(3):275-83. [PubMed:15252817 ]
  4. Sanelli TR, Sopper MM, Strong MJ: Sequestration of nNOS in neurofilamentous aggregate bearing neurons in vitro leads to enhanced NMDA-mediated calcium influx. Brain Res. 2004 Apr 9;1004(1-2):8-17. [PubMed:15033415 ]
  5. Weyermann J, Lochmann D, Georgens C, Zimmer A: Albumin-protamine-oligonucleotide-nanoparticles as a new antisense delivery system. Part 2: cellular uptake and effect. Eur J Pharm Biopharm. 2005 Apr;59(3):431-8. [PubMed:15760723 ]
  6. Baskys A, Blaabjerg M: Understanding regulation of nerve cell death by mGluRs as a method for development of successful neuroprotective strategies. J Neurol Sci. 2005 Mar 15;229-230:201-9. Epub 2004 Dec 15. [PubMed:15760640 ]
  7. Hardingham GE, Bading H: The Yin and Yang of NMDA receptor signalling. Trends Neurosci. 2003 Feb;26(2):81-9. [PubMed:12536131 ]
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