Showing metabocard for D-Arginine (BMDB0003416)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
Record Information
Version1.0
Creation Date2016-09-30 23:04:26 UTC
Update Date2020-05-21 16:28:31 UTC
BMDB IDBMDB0003416
Secondary Accession Numbers
  • BMDB03416
Metabolite Identification
Common NameD-Arginine
DescriptionD-Arginine, also known as D-arginine or DAR, belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom. D-Arginine is possibly soluble (in water) and a very strong basic compound (based on its pKa). D-Arginine can be converted into 2-oxoarginine through its interaction with the enzyme D-amino-acid oxidase. In cattle, D-argininee is involved in the metabolic pathway called the D-argininee and D-ornithine metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(2R)-2-Amino-5-(carbamimidamido)pentanoic acidChEBI
(2R)-2-Amino-5-guanidinopentanoic acidChEBI
(R)-2-Amino-5-guanidinopentanoic acidChEBI
D-2-Amino-5-guanidinovaleric acidChEBI
D-ArgininChEBI
DARChEBI
(2R)-2-Amino-5-(carbamimidamido)pentanoateGenerator
(2R)-2-Amino-5-guanidinopentanoateGenerator
(R)-2-Amino-5-guanidinopentanoateGenerator
D-2-Amino-5-guanidinovalerateGenerator
Chemical FormulaC6H14N4O2
Average Molecular Weight174.201
Monoisotopic Molecular Weight174.111675712
IUPAC Name(2R)-2-amino-5-carbamimidamidopentanoic acid
Traditional NameD-arginine
CAS Registry Number157-06-2
SMILES
N[C@H](CCCNC(N)=N)C(O)=O
InChI Identifier
InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/t4-/m1/s1
InChI KeyODKSFYDXXFIFQN-SCSAIBSYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentD-alpha-amino acids
Alternative Parents
Substituents
  • D-alpha-amino acid
  • Fatty acid
  • Guanidine
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Carboximidamide
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Peroxisome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.5ALOGPS
logP-3.2ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)2.41ChemAxon
pKa (Strongest Basic)12.41ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area125.22 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity53.92 m³·mol⁻¹ChemAxon
Polarizability18.04 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, Positivesplash10-00dl-9100000000-60db59de76b9a9b5bfc8View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00dl-9510000000-a5f3be057956f5efb0fdView in MoNA
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)splash10-00di-1900000000-a1207a353a5d383e8118View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00di-9000000000-38faac95afc81e981a08View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-00di-9000000000-776b9e0f6bf6a0ddf5baView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-1900000000-0627028bdd33e89ac545View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03mi-8900000000-d00d08306af5359ec3dcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-9000000000-09fdbc63550a3fe95638View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00e9-2900000000-4f23a56d70e700301134View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-053r-7900000000-02e7df28226010832ffeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-435f29993f2aaceb0d44View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-056r-0900000000-fe2cccae6934dad0053bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-9200000000-da3c09ec6a806e5c0777View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-9000000000-15e9d13a1d44b86b2a6cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-0900000000-a706f1985fb3e9e0adbbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-2900000000-b42c24606ae24000888dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-1c8520c5f7efb1187e43View 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
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Peroxisome
Biospecimen Locations
  • Epidermis
  • Platelet
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
EpidermisExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
PlateletExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0003416
DrugBank IDDB04027
Phenol Explorer Compound IDNot Available
FooDB IDFDB023167
KNApSAcK IDNot Available
Chemspider ID64224
KEGG Compound IDC00792
BioCyc IDCPD-220
BiGG ID36012
Wikipedia LinkArginine
METLIN ID6924
PubChem Compound71070
PDB IDNot Available
ChEBI ID15816
References
Synthesis ReferenceBirnbaum, Sanford M.; Winitz, Milton; Greenstein, Jesse P. A simplified preparation of D-arginine. Archives of Biochemistry and Biophysics (1956), 60 496-8.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. D-aspartate oxidase
General function:
Amino acid transport and metabolism
Specific function:
Not Available
Gene Name:
DDO
Uniprot ID:
P31228
Molecular weight:
37660.0
Reactions
D-Arginine + Water + Oxygen → 2-Oxoarginine + Ammonia + Hydrogen peroxidedetails