Np mrd loader

Record Information
Version1.0
Created at2020-11-23 18:24:57 UTC
Updated at2021-08-12 19:51:37 UTC
NP-MRD IDNP0002599
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Ornithine
Provided ByBMRBBMRB logo
DescriptionD-Ornithine 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. In humans, D-ornithine is involved in the d-arginine and d-ornithine metabolism pathway. D-Ornithine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. D-Ornithine is found in Mus musculus. It was first documented in 1997 (PMID: 16844612). Based on a literature review a significant number of articles have been published on D-Ornithine (PMID: 12557027) (PMID: 17984079) (PMID: 16753325) (PMID: 9887380).
Structure
Thumb
Synonyms
ValueSource
(R)-OrnithineChEBI
(2R)-2,5-DiaminopentanoateHMDB
(2R)-2,5-Diaminopentanoic acidHMDB
OrnithineHMDB
Ornithine monoacetate, (L)-isomerMeSH
Ornithine monohydrochloride, (D)-isomerMeSH
Ornithine monohydrochloride, (DL)-isomerMeSH
Ornithine phosphate (1:1), (L)-isomerMeSH
Ornithine sulfate (1:1), (L)-isomerMeSH
2,5 Diaminopentanoic acidMeSH
2,5-Diaminopentanoic acidMeSH
Ornithine dihydrochloride, (L)-isomerMeSH
Ornithine hydrochloride, (D)-isomerMeSH
Ornithine, (D)-isomerMeSH
Ornithine, (L)-isomerMeSH
Ornithine hydrochloride, (DL)-isomerMeSH
Ornithine hydrochloride, (L)-isomerMeSH
Ornithine monohydrobromide, (L)-isomerMeSH
Ornithine, (DL)-isomerMeSH
Chemical FormulaC5H12N2O2
Average Mass132.1610 Da
Monoisotopic Mass132.08988 Da
IUPAC Name(2R)-2,5-diaminopentanoic acid
Traditional NameL-(-)-ornithine
CAS Registry NumberNot Available
SMILES
NCCC[C@@H](N)C(O)=O
InChI Identifier
InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m1/s1
InChI KeyAHLPHDHHMVZTML-SCSAIBSYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Mus musculusLOTUS Database
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.6ALOGPS
logP-3.7ChemAxon
logS0.11ALOGPS
pKa (Strongest Acidic)2.67ChemAxon
pKa (Strongest Basic)10.29ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity33.21 m³·mol⁻¹ChemAxon
Polarizability13.74 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0003374
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023157
KNApSAcK IDNot Available
Chemspider ID64236
KEGG Compound IDC00515
BioCyc IDCPD-217
BiGG ID2263101
Wikipedia LinkOrnithine
METLIN ID6910
PubChem Compound71082
PDB IDNot Available
ChEBI ID16176
Good Scents IDNot Available
References
General References
  1. Filho JC, Bergstrom J, Stehle P, Furst P: Simultaneous measurements of free amino acid patterns of plasma, muscle and erythrocytes in healthy human subjects. Clin Nutr. 1997 Dec;16(6):299-305. [PubMed:16844612 ]
  2. Mayer UM: [Hyperornithinaemia in patients with retinal dystrophy]. Ophthalmologe. 2003 Jan;100(1):55-61. [PubMed:12557027 ]
  3. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
  4. Deignan JL, Livesay JC, Yoo PK, Goodman SI, O'Brien WE, Iyer RK, Cederbaum SD, Grody WW: Ornithine deficiency in the arginase double knockout mouse. Mol Genet Metab. 2006 Sep-Oct;89(1-2):87-96. doi: 10.1016/j.ymgme.2006.04.007. Epub 2006 Jun 5. [PubMed:16753325 ]
  5. Lauteala T, Mykkanen J, Sperandeo MP, Gasparini P, Savontaus ML, Simell O, Andria G, Sebastio G, Aula P: Genetic homogeneity of lysinuric protein intolerance. Eur J Hum Genet. 1998 Nov-Dec;6(6):612-5. doi: 10.1038/sj.ejhg.5200236. [PubMed:9887380 ]