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Showing metabocard for D-Arginine (HMDB0003416)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2006-08-12 20:28:49 UTC
Update Date2020-02-26 21:24:35 UTC
HMDB IDHMDB0003416
Secondary Accession Numbers
  • HMDB03416
Metabolite Identification
Common NameD-Arginine
DescriptionD-Arginine, also known as D-2-amino-5-guanidinovaleric acid or (2R)-2-amino-5-guanidinopentanoate, is a member of the class of compounds known as D-alpha-amino acids. D-alpha-Amino acids are alpha amino acids which have the D-configuration of the alpha-carbon atom. D-Arginine is slightly soluble (in water) and a moderately acidic compound (based on its pKa). D-Arginine can be found in human epidermis and platelet tissues. Within the cell, D-arginine is primarily located in the peroxisome. In humans, D-arginine is involved in D-arginine and D-ornithine metabolism. Arginine (abbreviated as Arg or R) is an alpha-amino acid that is used in the biosynthesis of proteins. It is encoded by the codons CGU, CGC, CGA, CGG, AGA, and AGG. It contains an alpha-amino group, an alpha-carboxylic acid group, and a side chain consisting of a 3-carbon aliphatic straight chain ending in a guanidino group. At physiological pH, the carboxylic acid is deprotonated (−COO−), the amino group is protonated (−NH3+), and the guanidino group is also protonated to give the guanidinium form (-C-(NH2)2+), making arginine a charged, aliphatic amino acid. It is the precursor for the biosynthesis of nitric oxide (Wikipedia ). D-Arginine is an essential amino acid that is physiologically active in the L-form.
Structure
Data?1582752275
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
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
Disposition

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility2.28 g/LALOGPS
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 FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00dl-9100000000-60db59de76b9a9b5bfc8Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00dl-9510000000-a5f3be057956f5efb0fdSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00di-1900000000-a1207a353a5d383e8118Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00di-9000000000-38faac95afc81e981a08Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-00di-9000000000-776b9e0f6bf6a0ddf5baSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-1900000000-0627028bdd33e89ac545Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03mi-8900000000-d00d08306af5359ec3dcSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-9000000000-09fdbc63550a3fe95638Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00e9-2900000000-4f23a56d70e700301134Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-053r-7900000000-02e7df28226010832ffeSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-435f29993f2aaceb0d44Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
Biological Properties
Cellular Locations
  • Peroxisome
Biospecimen LocationsNot Available
Tissue Locations
  • Epidermis
  • Platelet
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
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
Food Biomarker OntologyNot Available
VMH IDARG_D
MarkerDB ID
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)Download (PDF)
General References
  1. Hensel RR, King RC, Owens KG: Electrospray sample preparation for improved quantitation in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 1997;11(16):1785-93. [PubMed:9375412 ]
  2. Svedman P, Lundin S, Svedman C: Administration of antidiuretic peptide (DDAVP) by way of suction de-epithelialised skin. Lancet. 1991 Jun 22;337(8756):1506-9. [PubMed:1675370 ]
  3. Tulandi T, Yusuf N, Posner BI: Diabetes insipidus: a postpartum complication. Obstet Gynecol. 1987 Sep;70(3 Pt 2):492-5. [PubMed:3498136 ]
  4. van Lieburg AF, Verdijk MA, Schoute F, Ligtenberg MJ, van Oost BA, Waldhauser F, Dobner M, Monnens LA, Knoers NV: Clinical phenotype of nephrogenic diabetes insipidus in females heterozygous for a vasopressin type 2 receptor mutation. Hum Genet. 1995 Jul;96(1):70-8. [PubMed:7607658 ]
  5. Sorensen PS, Vilhardt H, Gjerris F, Warberg J: Impermeability of the blood-cerebrospinal fluid barrier to 1-deamino-8-D-arginine-vasopressin (DDAVP) in patients with acquired, communicating hydrocephalus. Eur J Clin Invest. 1984 Dec;14(6):435-9. [PubMed:6441719 ]
  6. Casonato A, Sartorello F, Cattini MG, Pontara E, Soldera C, Bertomoro A, Girolami A: An Arg760Cys mutation in the consensus sequence of the von Willebrand factor propeptide cleavage site is responsible for a new von Willebrand disease variant. Blood. 2003 Jan 1;101(1):151-6. Epub 2002 Aug 8. [PubMed:12393698 ]
  7. Ross MG, Cedars L, Nijland MJ, Ogundipe A: Treatment of oligohydramnios with maternal 1-deamino-[8-D-arginine] vasopressin-induced plasma hypoosmolality. Am J Obstet Gynecol. 1996 May;174(5):1608-13. [PubMed:9065138 ]
  8. Hochreutener H, Issakainen J, Bachmann C, Baerlocher K: [Carbamyl phosphate synthase deficiency: clinical symptoms, diagnosis and dietary-medicamentous treatment in the neonatal period and infancy]. Helv Paediatr Acta. 1989 Jun;43(5-6):493-505. [PubMed:2745145 ]
  9. Abiko T, Sekino H: Synthesis of an immunologically active fragment analog of prothymosin alpha with enhanced enzymatic stability. Chem Pharm Bull (Tokyo). 1991 Mar;39(3):752-6. [PubMed:2070460 ]
  10. Ritchie JL, Alexander HD, Allen P, Morgan D, McVeigh GE: Effect of nitric oxide modulation on systemic haemodynamics and platelet activation determined by P-selectin expression. Br J Haematol. 2002 Mar;116(4):892-8. [PubMed:11886397 ]

Enzymes

Enzyme Details
1. D-amino-acid oxidase
General function:
Involved in D-amino-acid oxidase activity
Specific function:
Regulates the level of the neuromodulator D-serine in the brain. Has high activity towards D-DOPA and contributes to dopamine synthesis. Could act as a detoxifying agent which removes D-amino acids accumulated during aging. Acts on a variety of D-amino acids with a preference for those having small hydrophobic side chains followed by those bearing polar, aromatic, and basic groups. Does not act on acidic amino acids.
Gene Name:
DAO
Uniprot ID:
P14920
Molecular weight:
39473.75