D-Ornithine (CHEM035518)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-05-26 05:50:34 UTC
Update Date2016-11-09 01:21:19 UTC
Accession NumberCHEM035518
Identification
Common NameD-Ornithine
ClassSmall Molecule
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. D-Ornithine is possibly soluble (in water) and a very strong basic compound (based on its pKa). D-Ornithine can be converted into 5-amino-2-oxopentanoic acid through its interaction with the enzyme D-amino-acid oxidase. In cattle, D-ornithine is involved in the metabolic pathway called the D-arginine and D-ornithine metabolism pathway.
Contaminant Sources
  • FooDB Chemicals
Contaminant TypeNot Available
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(R)-OrnithineChEBI
(2R)-2,5-DiaminopentanoateHMDB
(2R)-2,5-Diaminopentanoic acidHMDB
OrnithineHMDB
Chemical FormulaC5H12N2O2
Average Molecular Mass132.161 g/mol
Monoisotopic Mass132.090 g/mol
CAS Registry Number348-66-3
IUPAC Name(2R)-2,5-diaminopentanoic acid
Traditional NameL-(-)-ornithine
SMILESNCCC[C@@H](N)C(O)=O
InChI IdentifierInChI=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
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
Biological Properties
StatusDetected and Not Quantified
OriginNot Available
Cellular LocationsNot Available
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateNot Available
AppearanceNot Available
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
Predicted Properties
PropertyValueSource
Water Solubility172 g/LALOGPS
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001u-9000000000-deb45bcb4280a1e67a8fSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0089-9300000000-bbfdea03043e52ad8a15Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00lr-3900000000-1b22374231fec22d1e20Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00di-9300000000-0ce9f8eaa9b98ad18d91Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00di-9000000000-45d863665ba8a53004f0Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00di-9000000000-b4769e364cb748464ebeSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00di-9000000000-aaadcea853770440853cSpectrum
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-00di-9000000000-1aeb351c8832822b88f7Spectrum
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-00di-9000000000-64dc476dd1cd337386efSpectrum
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-00di-9000000000-ef7c20aed1e9a71b1432Spectrum
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-00di-9300000000-e36de55c16d7a2ed148fSpectrum
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-00xr-9700000000-a43025711954faa9935fSpectrum
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-00di-9000000000-1176f91c41c4400d1b5eSpectrum
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-00di-9000000000-f2bc6d43ca19a87e53abSpectrum
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-00xr-8900000000-03b469eaf5eacea319d6Spectrum
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-00di-9000000000-09147e6ddaef03f93f15Spectrum
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-001i-0900000000-0e3df57340c74126c5e7Spectrum
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-00b9-9000000000-d9ab801d36fbc1ca813fSpectrum
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-001i-3900000000-ae191a26241edfb2a693Spectrum
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-00di-9400000000-9e4d5ca58ccec4283d21Spectrum
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-00di-9000000000-8d64fc8fd06f41ed0f68Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-015i-7900000000-01f75740979c473383a0Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00dr-9100000000-8f2f412b16c89d59e236Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00dl-9000000000-a216a8d4439f992b205bSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-1900000000-59329678720e6407d762Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01qi-4900000000-8f53e4b8a940aa83cd3fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-9000000000-5cfb47a9082ed47a2fa1Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityNot Available
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)Not Available
Uses/SourcesNot Available
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsNot Available
TreatmentNot Available
Concentrations
Not Available
DrugBank IDNot Available
HMDB IDHMDB0003374
FooDB IDFDB023157
Phenol Explorer IDNot Available
KNApSAcK IDNot Available
BiGG ID2263101
BioCyc IDCPD-217
METLIN ID6910
PDB IDNot Available
Wikipedia LinkOrnithine
Chemspider ID64236
ChEBI ID16176
PubChem Compound ID71082
Kegg Compound IDC00515
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
1. Furui, Masakatsu; Takahashi, Eiji; Shibatani, Takeji. Microbial manufacture of D-amino acids from racemates. Jpn. Kokai Tokkyo Koho (1998), 13 pp.
2. 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. Epub 2006 Jun 5.
3. Mayer UM: [Hyperornithinaemia in patients with retinal dystrophy]. Ophthalmologe. 2003 Jan;100(1):55-61.
4. 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.
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.
6. Saito A, Noguchi Y, Yoshikawa T, Doi C, Fukuzawa K, Matsumoto A, Ito T, Tsuburaya A, Nagahara N: Gastrectomized patients are in a state of chronic protein malnutrition analyses of 23 amino acids. Hepatogastroenterology. 2001 Mar-Apr;48(38):585-9.
7. Nefyodov LI, Uglyanitsa KN, Smirnov VY, Karavay AV, Brzosko W: Comparative evaluation of blood plasma and tumor tissue amino acid pool in radiation or neoadjuvant preoperative therapies of breast cancer with the antitumor drug Ukrain. Drugs Exp Clin Res. 2000;26(5-6):231-7.
8. Rutten EP, Engelen MP, Schols AM, Deutz NE: Skeletal muscle glutamate metabolism in health and disease: state of the art. Curr Opin Clin Nutr Metab Care. 2005 Jan;8(1):41-51.
9. Vella S, Steiner F, Schlumbom V, Zurbrugg R, Wiesmann UN, Schaffner T, Wermuth B: Mutation of ornithine transcarbamylase (H136R) in a girl with severe intermittent orotic aciduria but normal enzyme activity. J Inherit Metab Dis. 1997 Aug;20(4):517-24.
10. Sela BA, Zlotnik J, Masos T, Yablonski G, Abraham F: [Gyrate atrophy of choroid and retina, and hyperornithinemia]. Harefuah. 2000 Jan 16;138(2):101-5, 175.
11. Camacho JA, Rioseco-Camacho N, Andrade D, Porter J, Kong J: Cloning and characterization of human ORNT2: a second mitochondrial ornithine transporter that can rescue a defective ORNT1 in patients with the hyperornithinemia-hyperammonemia-homocitrullinuria syndrome, a urea cycle disorder. Mol Genet Metab. 2003 Aug;79(4):257-71.
12. Monnier VM, Sell DR: Prevention and repair of protein damage by the Maillard reaction in vivo. Rejuvenation Res. 2006 Summer;9(2):264-73.
13. Zhang X, Rimpilainen M, Hoffmann B, Simelyte E, Aho H, Toivanen P: Experimental chronic arthritis and granulomatous inflammation induced by bifidobacterium cell walls. Scand J Immunol. 2001 Jul-Aug;54(1-2):171-9.
14. Jensen TG, Sullivan DM, Morgan RA, Taichman LB, Nussenblatt RB, Blaese RM, Csaky KG: Retrovirus-mediated gene transfer of ornithine-delta-aminotransferase into keratinocytes from gyrate atrophy patients. Hum Gene Ther. 1997 Nov 20;8(17):2125-32.
15. Sell DR, Monnier VM: Ornithine is a novel amino acid and a marker of arginine damage by oxoaldehydes in senescent proteins. Ann N Y Acad Sci. 2005 Jun;1043:118-28.
16. Gokmen SS, Aygit AC, Ayhan MS, Yorulmaz F, Gulen S: Significance of arginase and ornithine in malignant tumors of the human skin. J Lab Clin Med. 2001 May;137(5):340-4.
17. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043.
18. https://www.ncbi.nlm.nih.gov/pubmed/?term=21525873
19. https://www.ncbi.nlm.nih.gov/pubmed/?term=24326351
20. https://www.ncbi.nlm.nih.gov/pubmed/?term=24562332