Human Metabolome Database Version 3.5

Showing metabocard for Ornithine (HMDB00214)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-05-29 13:25:05 -0600
HMDB ID HMDB00214
Secondary Accession Numbers
  • HMDB00818
  • HMDB04984
Metabolite Identification
Common Name Ornithine
Description Ornithine 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 Link_out) 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 Link_out).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
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 Formula C5H12N2O2
Average Molecular Weight 132.161
Monoisotopic Molecular Weight 132.089877638
IUPAC Name (2S)-2,5-diaminopentanoic acid
Traditional IUPAC Name L-ornithine
CAS Registry Number 70-26-8
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 Key AHLPHDHHMVZTML-BYPYZUCNSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Amino Acids, Peptides, and Analogues
Class Amino Acids and Derivatives
Sub Class Alpha Amino Acids and Derivatives
Other Descriptors
  • Aliphatic Acyclic Compounds
  • alpha-amino acid(ChEBI)
Substituents
  • Carboxylic Acid
  • Polyamine
  • Primary Aliphatic Amine (Alkylamine)
Direct Parent Alpha Amino Acids and Derivatives
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Arginine and proline metabolism
  • Component of Glycine, serine and threonine metabolism
Application Not Available
Cellular locations
  • Extracellular
  • Mitochondria
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 140 °C Not Available
Boiling Point Not Available Not Available
Water Solubility 620 mg/mL Not Available
LogP -4.22 SANGSTER (1994)
Predicted Properties
Property Value Source
Water Solubility 172 g/L ALOGPS
LogP -3.64 ALOGPS
LogP -3.7 ChemAxon
LogS 0.11 ALOGPS
pKa (strongest acidic) 2.67 ChemAxon
pKa (strongest basic) 10.29 ChemAxon
Hydrogen Acceptor Count 4 ChemAxon
Hydrogen Donor Count 3 ChemAxon
Polar Surface Area 89.34 A2 ChemAxon
Rotatable Bond Count 4 ChemAxon
Refractivity 33.21 ChemAxon
Polarizability 13.94 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 1 ChemAxon
Spectra
Gas-MS Spectrum
1H NMR Spectrum
13C NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
[1H,1H] 2D NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue Location
  • Liver
  • Prostate
  • Skin
  • Gut
Pathways
Name SMPDB Link KEGG Link
Arginine and Proline Metabolism SMP00020 map00330 Link_out
Urea Cycle SMP00059 map00330 Link_out
Spermidine and Spermine Biosynthesis SMP00445 Not Available
Glycine and Serine Metabolism SMP00004 map00260 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
55.0 (39.0-71.0) uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
93.8 +/- 41.3 uM Adult (>18 years old) Not Specified Normal
Blood Detected and Quantified
90.0 +/- 20.0 uM Newborn (0-30 days old) Not Specified Normal
  • Geigy Scient...
Blood Detected and Quantified
47.0 +/- 14.0 uM Children (1-13 year old) Female Normal
  • Geigy Scient...
Blood Detected and Quantified
65.0 +/- 18.0 uM Adult (>18 years old) Male Normal
  • Geigy Scient...
Blood Detected and Quantified
54.0 +/- 18.0 uM Adult (>18 years old) Female Normal
  • Geigy Scient...
Blood Detected and Quantified
109.0 +/- 32.0 uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
34.3 +/- 13.0 uM Children (1-13 year old) Both Normal
Blood Detected and Quantified
66.9 +/- 15.3 uM Adult (>18 years old) Not Specified Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
4.87 (3.48-6.26) uM Adult (>18 years old) Both Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
8.3 +/- 4.7 uM Adult (>18 years old) Not Specified Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
6.0 +/- 1.5 uM Adult (>18 years old) Not Specified Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
4.9 +/- 1.6 uM Adult (>18 years old) Not Specified Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
3.7 +/- 1.0 uM Adult (>18 years old) Both Normal
  • Geigy Scient...
Cerebrospinal Fluid (CSF) Detected and Quantified
4.5 +/- 2.2 uM Adult (>18 years old) Not Specified Normal
Saliva Detected and Quantified
>10 uM Adult (>18 years old) Both Normal
Urine Detected and Quantified
5.3 (2.0-8.8) umol/mmol creatinine Adult (>18 years old) Both Comment Normal
Urine Detected and Quantified
0.98 umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected but not Quantified
Not Applicable Adult (>18 years old) Both Normal
Urine Detected and Quantified
5.0 (2.0-8.0) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
2.19 +/- 3.21 umol/mmol creatinine Infant (0-1 year old) Both Normal
Urine Detected and Quantified
2.0 (0.90-2.94) umol/mmol creatinine Adult (>18 years old) Male Normal
Urine Detected but not Quantified
Not Applicable Adult (>18 years old) Both Comment Normal
Urine Detected and Quantified
0.0024 - 0.0111 umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
0.987 (0.132-1.842) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
4.11 +/- 1.37 umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
4.4 (1.2-22.1) umol/mmol creatinine Adult (>18 years old) Both Comment Normal
Urine Detected and Quantified
0.050 (0.0-0.098) umol/mmol creatinine Newborn (0-30 days old) Both Normal
  • Geigy Scient...
  • West Cadwell...
  • Basel, Switz...
Urine Detected and Quantified
0.78 +/- 0.36 umol/mmol creatinine Children (1-13 year old) Male Normal
  • Geigy Scient...
  • West Cadwell...
  • Basel, Switz...
Urine Detected and Quantified
3.1 +/- 1.46 umol/mmol creatinine Adult (>18 years old) Male Normal
  • Geigy Scient...
  • West Cadwell...
  • Basel, Switz...
Urine Detected and Quantified
2.6 +/- 1.30 umol/mmol creatinine Adult (>18 years old) Female Normal
  • Geigy Scient...
  • West Cadwell...
  • Basel, Switz...
Urine Detected and Quantified
0.9 umol/mmol creatinine Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 65.4 +/- 30.4 uM Adult (>18 years old) Not Specified Heart Transplant
Blood Detected and Quantified 41.0 +/- 16.0 uM Adult (>18 years old) Both Ornithine transcarbamylase (OTC) deficiency
Blood Detected and Quantified 37.8 +/- 12.0 uM Children (1-13 year old) Both Uremia
Blood Detected and Quantified 68.35 +/- 22.43 uM Adult (>18 years old) Both Alzheimer's disease
Cerebrospinal Fluid (CSF) Detected and Quantified 7.6 +/- 3.1 uM Children (1-13 year old) Not Specified Leukemia
Cerebrospinal Fluid (CSF) Detected and Quantified 6.9 +/- 3.6 uM Children (1-13 year old) Not Specified Comment Leukemia
Urine Detected and Quantified 350.0 (200.0-500.0) umol/mmol creatinine Children (1-13 year old) Both Cystinuria
Urine Detected and Quantified 0.0025 - 0.0204 umol/mmol creatinine Adult (>18 years old) Both ADPKD
Urine Detected and Quantified 12.34 +/- 5.07 umol/mmol creatinine Adult (>18 years old) Both Alzheimer's disease
Urine Detected and Quantified 1285.00 (70.00-2500.00) umol/mmol creatinine Children (1-13 year old) Both Hyperdibasic aminoaciduria I
Urine Detected and Quantified 60.00 (20.00-100.00) umol/mmol creatinine Children (1-13 year old) Both Lysinuric protein intolerance
Associated Disorders and Diseases
Disease References
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 Link_out
      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 Link_out
          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 Link_out
              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 Link_out
                  Cystinuria
                      Hyperdibasic aminoaciduria I
                          Lysinuric protein intolerance
                              Associated OMIM IDs
                              DrugBank ID DB00129 Link_out
                              DrugBank Metabolite ID Not Available
                              Phenol Explorer Compound ID Not Available
                              Phenol Explorer Metabolite ID Not Available
                              FoodDB ID FDB003654
                              KNApSAcK ID Not Available
                              Chemspider ID 6026 Link_out
                              KEGG Compound ID C00077 Link_out
                              BioCyc ID L-ORNITHINE Link_out
                              BiGG ID 37976 Link_out
                              Wikipedia Link Ornithine Link_out
                              NuGOwiki Link HMDB00214 Link_out
                              Metagene Link HMDB00214 Link_out
                              METLIN ID 27 Link_out
                              PubChem Compound 6262 Link_out
                              PDB ID ORN Link_out
                              ChEBI ID 15729 Link_out
                              References
                              Synthesis Reference Zhang, 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. Mayer UM: [Hyperornithinaemia in patients with retinal dystrophy] Ophthalmologe. 2003 Jan;100(1):55-61. Pubmed: 12557027 Link_out
                              2. 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 Link_out
                              3. 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 Link_out
                              4. Gray RG, Green A, Hall S, McKeown C: Prenatal exclusion of the HHH syndrome. Prenat Diagn. 1995 May;15(5):474-6. Pubmed: 7644438 Link_out
                              5. 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 Link_out
                              6. 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 Link_out
                              7. 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 Link_out
                              8. 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 Link_out
                              9. 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 Link_out
                              10. 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 Link_out
                              11. 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 Link_out
                              12. 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 Link_out
                              13. 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 Link_out
                              14. 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 Link_out
                              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 Link_out

                              Enzymes
                              Name: Arginase-1
                              Reactions:
                              L-Arginine + Water unknown Ornithine + Urea details
                              Gene Name: ARG1
                              Uniprot ID: P05089 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Ornithine aminotransferase, mitochondrial
                              Reactions:
                              Ornithine + a 2-oxo acid unknown L-Glutamic gamma-semialdehyde + an L-amino acid details
                              Ornithine + Oxoglutaric acid unknown L-Glutamic gamma-semialdehyde + L-Glutamic acid details
                              Gene Name: OAT
                              Uniprot ID: P04181 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Glycine amidinotransferase, mitochondrial
                              Reactions:
                              L-Arginine + Glycine unknown Ornithine + Guanidoacetic acid details
                              L-Arginine + Gamma-Aminobutyric acid unknown Ornithine + 4-Guanidinobutanoic acid details
                              Gene Name: GATM
                              Uniprot ID: P50440 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Aminoacylase-1
                              Reactions:
                              N-Acetylornithine + Water unknown Acetic acid + Ornithine details
                              Gene Name: ACY1
                              Uniprot ID: Q03154 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Delta-1-pyrroline-5-carboxylate synthase
                              Reactions: Not Available
                              Gene Name: ALDH18A1
                              Uniprot ID: P54886 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Ornithine carbamoyltransferase, mitochondrial
                              Reactions:
                              Carbamoyl phosphate + Ornithine unknown Phosphoric acid + Citrulline details
                              Gene Name: OTC
                              Uniprot ID: P00480 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Ornithine decarboxylase
                              Reactions:
                              Ornithine unknown Putrescine + CO(2) details
                              Ornithine unknown Putrescine + Carbon dioxide details
                              Gene Name: ODC1
                              Uniprot ID: P11926 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Arginase-2, mitochondrial
                              Reactions:
                              L-Arginine + Water unknown Ornithine + Urea details
                              Gene Name: ARG2
                              Uniprot ID: P78540 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Cationic amino acid transporter 4
                              Reactions: Not Available
                              Gene Name: SLC7A4
                              Uniprot ID: O43246 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Mitochondrial ornithine transporter 1
                              Reactions: Not Available
                              Gene Name: SLC25A15
                              Uniprot ID: Q9Y619 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Mitochondrial ornithine transporter 2
                              Reactions: Not Available
                              Gene Name: SLC25A2
                              Uniprot ID: Q9BXI2 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Cationic amino acid transporter 3
                              Reactions: Not Available
                              Gene Name: SLC7A3
                              Uniprot ID: Q8WY07 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: High affinity cationic amino acid transporter 1
                              Reactions: Not Available
                              Gene Name: SLC7A1
                              Uniprot ID: P30825 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Low affinity cationic amino acid transporter 2
                              Reactions: Not Available
                              Gene Name: SLC7A2
                              Uniprot ID: P52569 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Y+L amino acid transporter 2
                              Reactions: Not Available
                              Gene Name: SLC7A6
                              Uniprot ID: Q92536 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Ornithine decarboxylase antizyme 1
                              Reactions: Not Available
                              Gene Name: OAZ1
                              Uniprot ID: P54368 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Ornithine decarboxylase antizyme 2
                              Reactions: Not Available
                              Gene Name: OAZ2
                              Uniprot ID: O95190 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Ornithine decarboxylase antizyme 3
                              Reactions: Not Available
                              Gene Name: OAZ3
                              Uniprot ID: Q9UMX2 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: Antizyme inhibitor 1
                              Reactions: Not Available
                              Gene Name: AZIN1
                              Uniprot ID: O14977 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA