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Record Information
Version3.6
Creation Date2006-08-12 19:50:22 UTC
Update Date2016-02-11 01:06:13 UTC
HMDB IDHMDB03374
Secondary Accession NumbersNone
Metabolite Identification
Common NameD-Ornithine
DescriptionD-Ornithine is an amino acid produced in the urea cycle by the splitting off of urea from arginine. Ornithine is one of the products of the action of the enzyme arginase on L-arginine, creating urea. Therefore, ornithine is a central part of the urea cycle, which allows for the disposal of excess nitrogen.
Structure
Thumb
Synonyms
ValueSource
(R)-OrnithineChEBI
(2R)-2,5-DiaminopentanoateGenerator
OrnithineHMDB
Chemical FormulaC5H12N2O2
Average Molecular Weight132.161
Monoisotopic Molecular Weight132.089877638
IUPAC Name(2R)-2,5-diaminopentanoic acid
Traditional NameL-(-)-ornithine
CAS Registry Number348-66-3
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 KeyInChIKey=AHLPHDHHMVZTML-SCSAIBSYSA-N
Chemical Taxonomy
DescriptionThis compound 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
  • Amino fatty acid
  • Fatty acyl
  • Fatty acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Arginine and proline metabolism
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
Water Solubility172.0 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity33.21 m3·mol-1ChemAxon
Polarizability13.74 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular Locations
  • Peroxisome
Biofluid Locations
  • Blood
  • Saliva
Tissue Location
  • Fibroblasts
  • Intestine
  • Liver
  • Muscle
  • Skeletal Muscle
  • Skin
  • Spleen
Pathways
NameSMPDB LinkKEGG Link
D-Arginine and D-Ornithine MetabolismSMP00036map00472
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified89.0 +/- 28.0 uMAdult (>18 years old)BothNormal details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified62.0 +/- 28.0 uMAdult (>18 years old)Both
Short bowel syndrome
details
Associated Disorders and Diseases
Disease References
Short bowel syndrome
  1. Pita AM, Fernandez-Bustos A, Rodes M, Arranz JA, Fisac C, Virgili N, Soler J, Wakabayashi Y: Orotic aciduria and plasma urea cycle-related amino acid alterations in short bowel syndrome, evoked by an arginine-free diet. JPEN J Parenter Enteral Nutr. 2004 Sep-Oct;28(5):315-23. [15449570 ]
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB023157
KNApSAcK IDNot Available
Chemspider ID64236
KEGG Compound IDC00515
BioCyc IDCPD-217
BiGG ID2263101
Wikipedia Linkornithine
NuGOwiki LinkHMDB03374
Metagene LinkHMDB03374
METLIN ID6910
PubChem Compound71082
PDB IDORD
ChEBI ID16176
References
Synthesis ReferenceFurui, Masakatsu; Takahashi, Eiji; Shibatani, Takeji. Microbial manufacture of D-amino acids from racemates. Jpn. Kokai Tokkyo Koho (1998), 13 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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. [12948741 ]
  2. Filho JC, Bergstrom J, Stehle P, Furst P: Simultaneous measurements of free amino acid patternsof plasma, muscle and erythrocytes in healthy human subjects. Clin Nutr. 1997 Dec;16(6):299-305. [16844612 ]
  3. Mayer UM: [Hyperornithinaemia in patients with retinal dystrophy] Ophthalmologe. 2003 Jan;100(1):55-61. [12557027 ]
  4. 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. [9414260 ]
  5. 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. [16037230 ]
  6. 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. [11329531 ]
  7. 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. [16753325 ]
  8. 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. [9887380 ]
  9. 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. [11379360 ]
  10. 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. [11345030 ]
  11. 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. [15585999 ]
  12. 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. [9266387 ]
  13. 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. [10883069 ]
  14. Monnier VM, Sell DR: Prevention and repair of protein damage by the Maillard reaction in vivo. Rejuvenation Res. 2006 Summer;9(2):264-73. [16706654 ]
  15. 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. [11439164 ]

Enzymes

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
Reactions
D-Ornithine + Water + Oxygen → 5-Amino-2-oxopentanoic acid + Ammonia + Hydrogen peroxidedetails