Showing metabocard for N-Methyl-D-aspartic acid (BMDB0002393)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (9) Show 9 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:55:01 UTC
Update Date2020-05-11 20:30:37 UTC
BMDB IDBMDB0002393
Secondary Accession Numbers
  • BMDB02393
Metabolite Identification
Common NameN-Methyl-D-aspartic acid
DescriptionN-Methyl-D-aspartic acid, also known as N-methylaspartate or (R)-2-methylamino-succinate, 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. N-Methyl-D-aspartic acid exists as a solid, possibly soluble (in water), and a very strong basic compound (based on its pKa) molecule.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
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
Acid, N-methyl-D-asparticMeSH
N Methyl D aspartateMeSH
N Methyl D aspartic acidMeSH
N MethylaspartateMeSH
N-Me-D-asp-OHHMDB
N-Methyl D-aspartateHMDB
N-Methyl D-aspartic acidHMDB
Chemical FormulaC5H9NO4
Average Molecular Weight147.1293
Monoisotopic Molecular Weight147.053157781
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
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
Ontology
StatusDetected but not Quantified
OriginNot Available
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point187 - 192 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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 FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0k96-9300000000-416b6ee56e62fb8e5961View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00dl-9410000000-4a49e66d4a20edeb3235View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-000i-9600000000-7a4c870f26f91384c5d0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-000f-9000000000-5a5c118fa9bc800c8c72View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0006-9000000000-b494ed61acdeddeb3be4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-0002-1900000000-87587cfe05ee404f1550View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0gba-1900000000-849defcb6a9a98faef16View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0gba-1900000000-9f82f9c552f606136a19View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0006-9000000000-b6e45215a0b6b9a0960fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-0007-9500000000-060344e1da8123dc5c51View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-bbf199eb1c5bbac7de35View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000i-9300000000-9f1996c5b204a0ee904eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000f-9000000000-18a491a74a3279ec33d1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-000l-9000000000-b9b082c40ee1ed6fbb8bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000i-9300000000-435580f32c2f9263f08fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-000f-9000000000-d6cd5876d7888f53004aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000i-9400000000-6e3a2b4573d59f5f903dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-69cb5c680dcf502b4d39View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-000l-9000000000-3b16cb5a635969b81fb4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-6e09556b565532cc28ceView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-000i-9600000000-f385ad30a0df8435d853View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0900000000-eeb3a907ee733c1543e9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f80-9600000000-1c3def640e73db97c7e4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9000000000-9f7de36da4128db64ccbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f6t-0900000000-6c4446f90caead6f5b51View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufs-3900000000-44106308c45837087fe5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0ac3-9100000000-fe891bbc2ab7063b8bacView in MoNA
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Brain
  • Fibroblasts
  • Kidney
  • Milk
  • Neuron
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BrainExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
FibroblastsExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
KidneyExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
NeuronExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0002393
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB 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
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Mung D, Li L: Development of Chemical Isotope Labeling LC-MS for Milk Metabolomics: Comprehensive and Quantitative Profiling of the Amine/Phenol Submetabolome. Anal Chem. 2017 Apr 18;89(8):4435-4443. doi: 10.1021/acs.analchem.6b03737. Epub 2017 Mar 28. [PubMed:28306241 ]

Enzymes

Enzyme Details
1. Platelet-activating factor acetylhydrolase IB subunit alpha
General function:
Involved in dynactin binding
Specific function:
Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes such as the maintenance of Golgi integrity, the peripheral transport of microtubule fragments and the coupling of the nucleus and centrosome. Required during brain development for the proliferation of neuronal precursors and the migration of newly formed neurons from the ventricular/subventricular zone toward the cortical plate. Neuronal migration involves a process called nucleokinesis, whereby migrating cells extend an anterior process into which the nucleus subsequently translocates. During nucleokinesis dynein at the nuclear surface may translocate the nucleus towards the centrosome by exerting force on centrosomal microtubules. Also required for proper activation of Rho GTPases and actin polymerization at the leading edge of locomoting cerebellar neurons and postmigratory hippocampal neurons in response to calcium influx triggered via NMDA receptors. May also play a role in other forms of cell locomotion including the migration of fibroblasts during wound healing (By similarity). Non-catalytic subunit of an acetylhydrolase complex which inactivates platelet-activating factor (PAF) by removing the acetyl group at the SN-2 position. Required for pronuclear migration during fertilization. Required for dynein recruitment to microtubule plus ends and BICD2-bound cargos (By similarity).
Gene Name:
PAFAH1B1
Uniprot ID:
P43033
Molecular weight:
46613.0
Enzyme Details
2. Solute carrier family 22 member 1
General function:
Carbohydrate transport and metabolism
Specific function:
Translocates a broad array of organic cations with various structures and molecular weights including the model compounds 1-methyl-4-phenylpyridinium (MPP), tetraethylammonium (TEA), N-1-methylnicotinamide (NMN), 4-(4-(dimethylamino)styryl)-N-methylpyridinium (ASP), the endogenous compounds choline, guanidine, histamine, epinephrine, adrenaline, noradrenaline and dopamine, and the drugs quinine, and metformin. The transport of organic cations is inhibited by a broad array of compounds like tetramethylammonium (TMA), cocaine, lidocaine, NMDA receptor antagonists, atropine, prazosin, cimetidine, TEA and NMN, guanidine, cimetidine, choline, procainamide, quinine, tetrabutylammonium, and tetrapentylammonium. Translocates organic cations in an electrogenic and pH-independent manner. Translocates organic cations across the plasma membrane in both directions. Transports the polyamines spermine and spermidine. Transports pramipexole across the basolateral membrane of the proximal tubular epithelial cells. The choline transport is activated by MMTS. Regulated by various intracellular signaling pathways including inhibition by protein kinase A activation, and endogenously activation by the calmodulin complex, the calmodulin-dependent kinase II and LCK tyrosine kinase (By similarity).
Gene Name:
SLC22A1
Uniprot ID:
A7MBE0
Molecular weight:
62502.0
Enzyme Details
3. Calcium-binding protein 1
General function:
Involved in calcium ion binding
Specific function:
Modulates calcium-dependent activity of inositol 1,4,5-triphosphate receptors (ITPRs). Inhibits agonist-induced intracellular calcium signaling. Enhances inactivation and does not support calcium-dependent facilitation of voltage-dependent P/Q-type calcium channels. Causes calcium-dependent facilitation and inhibits inactivation of L-type calcium channels by binding to the same sites as calmodulin in the C-terminal domain of CACNA1C, but has an opposite effect on channel function. Suppresses the calcium-dependent inactivation of CACNA1D. Inhibits TRPC5 channels. Prevents NMDA receptor-induced cellular degeneration. Required for the normal transfer of light signals through the retina.
Gene Name:
CABP1
Uniprot ID:
Q9N1R0
Molecular weight:
25755.0
Enzyme Details
4. Little elongation complex subunit 2
General function:
Not Available
Specific function:
Component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III.
Gene Name:
ICE2
Uniprot ID:
Q0VCQ7
Molecular weight:
109914.0
Enzyme Details
5. Protein lifeguard 1
General function:
Not Available
Specific function:
Potential apoptotic regulator.
Gene Name:
GRINA
Uniprot ID:
Q32L53
Molecular weight:
40232.0
Enzyme Details
6. Protein lin-7 homolog C
General function:
Involved in exocytosis
Specific function:
Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells. Forms membrane-associated multiprotein complexes that may regulate delivery and recycling of proteins to the correct membrane domains. The tripartite complex composed of LIN7 (LIN7A, LIN7B or LIN7C), CASK and APBA1 may have the potential to couple synaptic vesicle exocytosis to cell adhesion in brain. Ensures the proper localization of GRIN2B (subunit 2B of the NMDA receptor) to neuronal postsynaptic density and may function in localizing synaptic vesicles at synapses where it is recruited by beta-catenin and cadherin. Required to localize Kir2 channels, GABA transporter (SLC6A12) and EGFR/ERBB1, ERBB2, ERBB3 and ERBB4 to the basolateral membrane of epithelial cells (By similarity).
Gene Name:
LIN7C
Uniprot ID:
Q0P5F3
Molecular weight:
21834.0
Enzyme Details
7. Protein lin-7 homolog B
General function:
Involved in protein binding
Specific function:
Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells. Forms membrane-associated multiprotein complexes that may regulate delivery and recycling of proteins to the correct membrane domains. The tripartite complex composed of LIN7 (LIN7A, LIN7B or LIN7C), CASK and APBA1 may have the potential to couple synaptic vesicle exocytosis to cell adhesion in brain. Ensures the proper localization of GRIN2B (subunit 2B of the NMDA receptor) to neuronal postsynaptic density and may function in localizing synaptic vesicles at synapses where it is recruited by beta-catenin and cadherin. Required to localize Kir2 channels, GABA transporter (SLC6A12) and EGFR/ERBB1, ERBB2, ERBB3 and ERBB4 to the basolateral membrane of epithelial cells. May increase the amplitude of ASIC3 acid-evoked currents by stabilizing the channel at the cell surface (By similarity).
Gene Name:
LIN7B
Uniprot ID:
Q2KIB6
Molecular weight:
22280.0
Enzyme Details
8. Protein lin-7 homolog A
General function:
Involved in protein binding
Specific function:
Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells. Forms membrane-associated multiprotein complexes that may regulate delivery and recycling of proteins to the correct membrane domains. The tripartite complex composed of LIN7 (LIN7A, LIN7B or LIN7C), CASK and APBA1 may have the potential to couple synaptic vesicle exocytosis to cell adhesion in brain. Ensures the proper localization of GRIN2B (subunit 2B of the NMDA receptor) to neuronal postsynaptic density and may function in localizing synaptic vesicles at synapses where it is recruited by beta-catenin and cadherin. Required to localize Kir2 channels, GABA transporter (SLC6A12) and EGFR/ERBB1, ERBB2, ERBB3 and ERBB4 to the basolateral membrane of epithelial cells (By similarity).
Gene Name:
LIN7A
Uniprot ID:
Q32LM6
Molecular weight:
25997.0
Enzyme Details
9. Sodium- and chloride-dependent glycine transporter 1
General function:
Involved in neurotransmitter:sodium symporter activity
Specific function:
Terminates the action of glycine by its high affinity sodium-dependent reuptake into presynaptic terminals. May play a role in regulation of glycine levels in NMDA receptor-mediated neurotransmission (By similarity).
Gene Name:
SLC6A9
Uniprot ID:
Q28039
Molecular weight:
71318.0