Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2013-05-29 19:25:05 UTC
HMDB IDHMDB00214
Secondary Accession Numbers
  • HMDB00818
  • HMDB04984
Metabolite Identification
Common NameOrnithine
DescriptionOrnithine is an amino acid produced in the urea cycle by the splitting off of urea from arginine. It is a central part of the urea cycle, which allows for the disposal of excess nitrogen. L-Ornithine is also a precursor of citrulline and arginine. In order for ornithine produced in the cytosol to be converted to citrulline, it must first cross the inner mitochondrial membrane into the mitochondrial matrix where it is carbamylated by ornithine transcarbamylase. This transfer is mediated by the mitochondrial ornithine transporter (SLC25A15; AF112968; ORNT1). Mutations in the mitochondrial ornithine transporter result in hyperammonemia, hyperornithinemia, homocitrullinuria (HHH) syndrome, a disorder of the urea cycle. (PMID 16256388 ) The pathophysiology of the disease may involve diminished ornithine transport into mitochondria, resulting in ornithine accumulation in the cytoplasm and reduced ability to clear carbamoyl phosphate and ammonia loads. (OMIM 838970 ).
Structure
Thumb
Synonyms
  1. (+)-S-Ornithine
  2. (S)-2,5-Diaminopentanoate
  3. (S)-2,5-Diaminopentanoic acid
  4. (S)-a,D-Diaminovalerate
  5. (S)-a,D-Diaminovaleric acid
  6. (S)-Ornithine
  7. 5-Amino-L-Norvaline
  8. L-(-)-Ornithine
  9. L-Ornithine
Chemical FormulaC5H12N2O2
Average Molecular Weight132.161
Monoisotopic Molecular Weight132.089877638
IUPAC Name(2S)-2,5-diaminopentanoic acid
Traditional IUPAC NameL-ornithine
CAS Registry Number70-26-8
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-/m0/s1
InChI KeyAHLPHDHHMVZTML-BYPYZUCNSA-N
Chemical Taxonomy
KingdomOrganic Compounds
Super ClassAmino Acids, Peptides, and Analogues
ClassAmino Acids and Derivatives
Sub ClassAlpha Amino Acids and Derivatives
Other Descriptors
  • Aliphatic Acyclic Compounds
  • alpha-amino acid(ChEBI)
Substituents
  • Carboxylic Acid
  • Polyamine
  • Primary Aliphatic Amine (Alkylamine)
Direct ParentAlpha Amino Acids and Derivatives
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Arginine and proline metabolism
  • Component of Glycine, serine and threonine metabolism
ApplicationNot Available
Cellular locations
  • Extracellular
  • Mitochondria
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point140 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility620 mg/mLNot Available
LogP-4.22SANGSTER (1994)
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 area89.34ChemAxon
rotatable bond count4ChemAxon
refractivity33.21ChemAxon
polarizability13.94ChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue Location
  • Gut
  • Liver
  • Prostate
  • Skin
Pathways
NameSMPDB LinkKEGG Link
Arginine and Proline MetabolismSMP00020map00330
Glycine and Serine MetabolismSMP00004map00260
Spermidine and Spermine BiosynthesisSMP00445Not Available
Urea CycleSMP00059map00330
Normal Concentrations
BiofluidStatusValueAgeSexConditionReference
BloodDetected and Quantified55.0 (39.0-71.0) uMAdult (>18 years old)BothNormal
BloodDetected and Quantified93.8 +/- 41.3 uMAdult (>18 years old)Not SpecifiedNormal
BloodDetected and Quantified90.0 +/- 20.0 uMNewborn (0-30 days old)Not SpecifiedNormal
  • Geigy Scient...
BloodDetected and Quantified47.0 +/- 14.0 uMChildren (1-13 year old)FemaleNormal
  • Geigy Scient...
BloodDetected and Quantified65.0 +/- 18.0 uMAdult (>18 years old)MaleNormal
  • Geigy Scient...
BloodDetected and Quantified54.0 +/- 18.0 uMAdult (>18 years old)FemaleNormal
  • Geigy Scient...
BloodDetected and Quantified109.0 +/- 32.0 uMAdult (>18 years old)BothNormal
BloodDetected and Quantified34.3 +/- 13.0 uMChildren (1-13 year old)BothNormal
BloodDetected and Quantified66.9 +/- 15.3 uMAdult (>18 years old)Not SpecifiedNormal
Cerebrospinal Fluid (CSF)Detected and Quantified4.87 (3.48-6.26) uMAdult (>18 years old)BothNormal
Cerebrospinal Fluid (CSF)Detected and Quantified8.3 +/- 4.7 uMAdult (>18 years old)Not SpecifiedNormal
Cerebrospinal Fluid (CSF)Detected and Quantified6.0 +/- 1.5 uMAdult (>18 years old)Not SpecifiedNormal
Cerebrospinal Fluid (CSF)Detected and Quantified4.9 +/- 1.6 uMAdult (>18 years old)Not SpecifiedNormal
Cerebrospinal Fluid (CSF)Detected and Quantified3.7 +/- 1.0 uMAdult (>18 years old)BothNormal
  • Geigy Scient...
Cerebrospinal Fluid (CSF)Detected and Quantified4.5 +/- 2.2 uMAdult (>18 years old)Not SpecifiedNormal
SalivaDetected and Quantified>10 uMAdult (>18 years old)BothNormal
UrineDetected and Quantified5.3 (2.0-8.8) umol/mmol creatinineAdult (>18 years old)BothCommentNormal
UrineDetected and Quantified0.98 umol/mmol creatinineAdult (>18 years old)BothNormal
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)BothNormal
UrineDetected and Quantified5.0 (2.0-8.0) umol/mmol creatinineAdult (>18 years old)BothNormal
UrineDetected and Quantified2.19 +/- 3.21 umol/mmol creatinineInfant (0-1 year old)BothNormal
UrineDetected and Quantified2.0 (0.90-2.94) umol/mmol creatinineAdult (>18 years old)MaleNormal
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)BothCommentNormal
UrineDetected and Quantified0.0024 - 0.0111 umol/mmol creatinineAdult (>18 years old)BothNormal
UrineDetected and Quantified0.987 (0.132-1.842) umol/mmol creatinineAdult (>18 years old)BothNormal
    UrineDetected and Quantified4.11 +/- 1.37 umol/mmol creatinineAdult (>18 years old)BothNormal
    UrineDetected and Quantified4.4 (1.2-22.1) umol/mmol creatinineAdult (>18 years old)BothCommentNormal
    UrineDetected and Quantified0.050 (0.0-0.098) umol/mmol creatinineNewborn (0-30 days old)BothNormal
    • Geigy Scient...
    • West Cadwell...
    • Basel, Switz...
    UrineDetected and Quantified0.78 +/- 0.36 umol/mmol creatinineChildren (1-13 year old)MaleNormal
    • Geigy Scient...
    • West Cadwell...
    • Basel, Switz...
    UrineDetected and Quantified3.1 +/- 1.46 umol/mmol creatinineAdult (>18 years old)MaleNormal
    • Geigy Scient...
    • West Cadwell...
    • Basel, Switz...
    UrineDetected and Quantified2.6 +/- 1.30 umol/mmol creatinineAdult (>18 years old)FemaleNormal
    • Geigy Scient...
    • West Cadwell...
    • Basel, Switz...
    UrineDetected and Quantified0.9 umol/mmol creatinineAdult (>18 years old)BothNormal
    Abnormal Concentrations
    BiofluidStatusValueAgeSexConditionReference
    BloodDetected and Quantified65.4 +/- 30.4 uMAdult (>18 years old)Not SpecifiedHeart Transplant
    BloodDetected and Quantified41.0 +/- 16.0 uMAdult (>18 years old)BothOrnithine transcarbamylase (OTC) deficiency
    BloodDetected and Quantified37.8 +/- 12.0 uMChildren (1-13 year old)BothUremia
    BloodDetected and Quantified68.35 +/- 22.43 uMAdult (>18 years old)BothAlzheimer's disease
    Cerebrospinal Fluid (CSF)Detected and Quantified7.6 +/- 3.1 uMChildren (1-13 year old)Not SpecifiedLeukemia
    Cerebrospinal Fluid (CSF)Detected and Quantified6.9 +/- 3.6 uMChildren (1-13 year old)Not SpecifiedCommentLeukemia
    UrineDetected and Quantified350.0 (200.0-500.0) umol/mmol creatinineChildren (1-13 year old)BothCystinuria
    UrineDetected and Quantified0.0025 - 0.0204 umol/mmol creatinineAdult (>18 years old)BothADPKD
    UrineDetected and Quantified12.34 +/- 5.07 umol/mmol creatinineAdult (>18 years old)BothAlzheimer's disease
    UrineDetected and Quantified1285.00 (70.00-2500.00) umol/mmol creatinineChildren (1-13 year old)BothHyperdibasic aminoaciduria I
    UrineDetected and Quantified60.00 (20.00-100.00) umol/mmol creatinineChildren (1-13 year old)BothLysinuric protein intolerance
    Associated Disorders and Diseases
    Disease References
    Alzheimer's disease
    • Fonteh AN, Harrington RJ, Tsai A, Liao P, Harrington MG: Free amino acid and dipeptide changes in the body fluids from Alzheimer's disease subjects. Amino Acids. 2007 Feb;32(2):213-24. Epub 2006 Oct 10. Pubmed: 17031479
    Cystinuria
    Leukemia
    • Peng CT, Wu KH, Lan SJ, Tsai JJ, Tsai FJ, Tsai CH: Amino acid concentrations in cerebrospinal fluid in children with acute lymphoblastic leukemia undergoing chemotherapy. Eur J Cancer. 2005 May;41(8):1158-63. Epub 2005 Apr 14. Pubmed: 15911239
    Lysinuric protein intolerance
    Ornithine transcarbamylase deficiency
    • Harada E, Nishiyori A, Tokunaga Y, Watanabe Y, Kuriya N, Kumashiro R, Kuno T, Kuromaru R, Hirose S, Ichikawa K, Yoshino M: Late-onset ornithine transcarbamylase deficiency in male patients: prognostic factors and characteristics of plasma amino acid profile. Pediatr Int. 2006 Apr;48(2):105-11. Pubmed: 16635166
    Uremia
    • Canepa A, Filho JC, Gutierrez A, Carrea A, Forsberg AM, Nilsson E, Verrina E, Perfumo F, Bergstrom J: Free amino acids in plasma, red blood cells, polymorphonuclear leukocytes, and muscle in normal and uraemic children. Nephrol Dial Transplant. 2002 Mar;17(3):413-21. Pubmed: 11865086
    Hyperdibasic aminoaciduria I
    Associated OMIM IDs
    DrugBank IDDB00129
    DrugBank Metabolite IDNot Available
    Phenol Explorer Compound IDNot Available
    Phenol Explorer Metabolite IDNot Available
    FoodDB IDFDB003654
    KNApSAcK IDNot Available
    Chemspider ID6026
    KEGG Compound IDC00077
    BioCyc IDL-ORNITHINE
    BiGG ID37976
    Wikipedia LinkOrnithine
    NuGOwiki LinkHMDB00214
    Metagene LinkHMDB00214
    METLIN ID27
    PubChem Compound6262
    PDB IDORN
    ChEBI ID15729
    References
    Synthesis ReferenceZhang, Peng; Zhang, Shurong; Liu, Chunqiao; Yang, Yuhong. Method for preparing L-ornithine by enzymatic conversion. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 8pp.
    Material Safety Data Sheet (MSDS)Download (PDF)
    General References
    1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
    2. Silwood CJ, Lynch E, Claxson AW, Grootveld MC: 1H and (13)C NMR spectroscopic analysis of human saliva. J Dent Res. 2002 Jun;81(6):422-7. Pubmed: 12097436
    3. Nicholson JK, O'Flynn MP, Sadler PJ, Macleod AF, Juul SM, Sonksen PH: Proton-nuclear-magnetic-resonance studies of serum, plasma and urine from fasting normal and diabetic subjects. Biochem J. 1984 Jan 15;217(2):365-75. Pubmed: 6696735
    4. Engelborghs S, Marescau B, De Deyn PP: Amino acids and biogenic amines in cerebrospinal fluid of patients with Parkinson's disease. Neurochem Res. 2003 Aug;28(8):1145-50. Pubmed: 12834252
    5. Hagenfeldt L, Bjerkenstedt L, Edman G, Sedvall G, Wiesel FA: Amino acids in plasma and CSF and monoamine metabolites in CSF: interrelationship in healthy subjects. J Neurochem. 1984 Mar;42(3):833-7. Pubmed: 6198473
    6. Peng CT, Wu KH, Lan SJ, Tsai JJ, Tsai FJ, Tsai CH: Amino acid concentrations in cerebrospinal fluid in children with acute lymphoblastic leukemia undergoing chemotherapy. Eur J Cancer. 2005 May;41(8):1158-63. Epub 2005 Apr 14. Pubmed: 15911239
    7. Cynober LA: Plasma amino acid levels with a note on membrane transport: characteristics, regulation, and metabolic significance. Nutrition. 2002 Sep;18(9):761-6. Pubmed: 12297216
    8. Peters T, Thaete C, Wolf S, Popp A, Sedlmeier R, Grosse J, Nehls MC, Russ A, Schlueter V: A mouse model for cystinuria type I. Hum Mol Genet. 2003 Sep 1;12(17):2109-20. Pubmed: 12923163
    9. Mayer UM: [Hyperornithinaemia in patients with retinal dystrophy] Ophthalmologe. 2003 Jan;100(1):55-61. Pubmed: 12557027
    10. Gray RG, Green A, Hall S, McKeown C: Prenatal exclusion of the HHH syndrome. Prenat Diagn. 1995 May;15(5):474-6. Pubmed: 7644438
    11. 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. Pubmed: 9414260
    12. 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. Pubmed: 16037230
    13. Stadler S, Gempel K, Bieger I, Pontz BF, Gerbitz KD, Bauer MF, Hofmann S: Detection of neonatal argininosuccinate lyase deficiency by serum tandem mass spectrometry. J Inherit Metab Dis. 2001 Jun;24(3):370-8. Pubmed: 11486903
    14. 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. Pubmed: 11329531
    15. Morizono H, Woolston JE, Colombini M, Tuchman M: The use of yeast mitochondria to study the properties of wild-type and mutant human mitochondrial ornithine transporter. Mol Genet Metab. 2005 Dec;86(4):431-40. Epub 2005 Oct 26. Pubmed: 16256388

    Enzymes

    Gene Name:
    ARG1
    Uniprot ID:
    P05089
    Reactions
    L-Arginine + Water unknown Ornithine + Ureadetails
    Gene Name:
    OAT
    Uniprot ID:
    P04181
    Reactions
    Ornithine + a 2-oxo acid unknown L-Glutamic gamma-semialdehyde + an L-amino aciddetails
    Ornithine + Oxoglutaric acid unknown L-Glutamic gamma-semialdehyde + L-Glutamic aciddetails
    Gene Name:
    GATM
    Uniprot ID:
    P50440
    Reactions
    L-Arginine + Glycine unknown Ornithine + Guanidoacetic aciddetails
    L-Arginine + Gamma-Aminobutyric acid unknown Ornithine + 4-Guanidinobutanoic aciddetails
    Gene Name:
    ACY1
    Uniprot ID:
    Q03154
    Reactions
    N-Acetylornithine + Water unknown Acetic acid + Ornithinedetails
    Gene Name:
    ALDH18A1
    Uniprot ID:
    P54886
    Gene Name:
    OTC
    Uniprot ID:
    P00480
    Reactions
    Carbamoyl phosphate + Ornithine unknown Phosphoric acid + Citrullinedetails
    Gene Name:
    ODC1
    Uniprot ID:
    P11926
    Reactions
    Ornithine unknown Putrescine + CO(2)details
    Ornithine unknown Putrescine + Carbon dioxidedetails
    Gene Name:
    ARG2
    Uniprot ID:
    P78540
    Reactions
    L-Arginine + Water unknown Ornithine + Ureadetails
    Gene Name:
    SLC7A4
    Uniprot ID:
    O43246
    Gene Name:
    SLC25A15
    Uniprot ID:
    Q9Y619
    Gene Name:
    SLC25A2
    Uniprot ID:
    Q9BXI2
    Gene Name:
    SLC7A3
    Uniprot ID:
    Q8WY07
    Gene Name:
    SLC7A6
    Uniprot ID:
    Q92536
    Gene Name:
    OAZ1
    Uniprot ID:
    P54368
    Gene Name:
    OAZ2
    Uniprot ID:
    O95190
    Gene Name:
    OAZ3
    Uniprot ID:
    Q9UMX2
    Gene Name:
    AZIN1
    Uniprot ID:
    O14977