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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-12 19:50:22 UTC
Update Date2021-09-14 15:45:46 UTC
HMDB IDHMDB0003374
Secondary Accession Numbers
  • HMDB03374
Metabolite Identification
Common NameD-Ornithine
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 a very strong basic compound (based on its pKa). D-ornithine can be converted into 5-amino-2-oxopentanoic acid through the action of the enzyme D-amino-acid oxidase. In humans, D-ornithine is involved in d-arginine and d-ornithine metabolism. Outside of the human body, D-Ornithine has been detected, but not quantified in, several different foods, such as cow milks, cow milks, cow milks, and cow milks. This could make D-ornithine a potential biomarker for the consumption of these foods. The D-enantiomer of ornithine.
Structure
Data?1582752273
Synonyms
ValueSource
(R)-OrnithineChEBI
(2R)-2,5-DiaminopentanoateHMDB
(2R)-2,5-Diaminopentanoic acidHMDB
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 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
Ontology
Physiological effect

Adverse health effect

Disposition

Biological location

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Spectral Properties

Experimental Collision Cross Sections

PredictorAdduct TypeData SourceCCS Value (Å2)Reference
DeepCCS[M-H]-MetCCS_train_neg126.73930932474
AllCCS[M-H]-Not Available128.3http://allccs.zhulab.cn/database/detail?ID=AllCCS00000057
AllCCS[M+H]+Not Available127.7http://allccs.zhulab.cn/database/detail?ID=AllCCS00000057
Predicted Molecular Properties
PropertyValueSource
Water Solubility172 g/LALOGPS
logP10(-3.6) g/LALOGPS
logP10(-3.7) g/LChemAxon
logS10(0.11) g/LALOGPS
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
Predicted Spectral Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+128.62831661259
DarkChem[M-H]-124.43531661259

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
D-Ornithine,1TMS,#1C[Si](C)(C)OC(=O)[C@H](N)CCCN1369.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Ornithine,1TMS,#2C[Si](C)(C)NCCC[C@@H](N)C(=O)O1525.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Ornithine,1TMS,#3C[Si](C)(C)N[C@H](CCCN)C(=O)O1479.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Ornithine,1TBDMS,#1CC(C)(C)[Si](C)(C)OC(=O)[C@H](N)CCCN1600.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Ornithine,1TBDMS,#2CC(C)(C)[Si](C)(C)NCCC[C@@H](N)C(=O)O1785.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Ornithine,1TBDMS,#3CC(C)(C)[Si](C)(C)N[C@H](CCCN)C(=O)O1729.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - D-Ornithine GC-MS (Non-derivatized) - 70eV, Positivesplash10-001u-9000000000-deb45bcb4280a1e67a8f2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ornithine GC-MS (1 TMS) - 70eV, Positivesplash10-0089-9300000000-bbfdea03043e52ad8a152017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ornithine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ornithine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 20V, Negative-QTOFsplash10-00di-9000000000-09147e6ddaef03f93f152021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 35V, Negative-QTOFsplash10-001i-0900000000-0e3df57340c74126c5e72021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 40V, Negative-QTOFsplash10-00b9-9000000000-d9ab801d36fbc1ca813f2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 10V, Negative-QTOFsplash10-001i-3900000000-ae191a26241edfb2a6932021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine LC-ESI-QQ , positive-QTOFsplash10-00lr-3900000000-1b22374231fec22d1e202017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine LC-ESI-QQ , positive-QTOFsplash10-00di-9300000000-0ce9f8eaa9b98ad18d912017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine LC-ESI-QQ , positive-QTOFsplash10-00di-9000000000-45d863665ba8a53004f02017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine LC-ESI-QQ , positive-QTOFsplash10-00di-9000000000-b4769e364cb748464ebe2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine LC-ESI-QQ , positive-QTOFsplash10-00di-9000000000-aaadcea853770440853c2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 40V, Positive-QTOFsplash10-00di-9000000000-1aeb351c8832822b88f72021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 40V, Positive-QTOFsplash10-00di-9000000000-64dc476dd1cd337386ef2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 20V, Positive-QTOFsplash10-00di-9000000000-ef7c20aed1e9a71b14322021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 10V, Positive-QTOFsplash10-00di-9300000000-e36de55c16d7a2ed148f2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 10V, Positive-QTOFsplash10-00xr-9700000000-a43025711954faa9935f2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 20V, Positive-QTOFsplash10-00di-9000000000-1176f91c41c4400d1b5e2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 40V, Positive-QTOFsplash10-00di-9000000000-f2bc6d43ca19a87e53ab2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 35V, Positive-QTOFsplash10-00xr-8900000000-03b469eaf5eacea319d62021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 10V, Positive-QTOFsplash10-00di-9400000000-9e4d5ca58ccec4283d212021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - D-Ornithine 20V, Positive-QTOFsplash10-00di-9000000000-8d64fc8fd06f41ed0f682021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ornithine 10V, Negative-QTOFsplash10-001i-1900000000-59329678720e6407d7622017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ornithine 20V, Negative-QTOFsplash10-01qi-4900000000-8f53e4b8a940aa83cd3f2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ornithine 40V, Negative-QTOFsplash10-00di-9000000000-5cfb47a9082ed47a2fa12017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ornithine 10V, Negative-QTOFsplash10-001i-0900000000-a7a55bed1d490bf8ce9c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ornithine 20V, Negative-QTOFsplash10-001i-0900000000-7bdea17348308c73bdcb2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ornithine 40V, Negative-QTOFsplash10-0006-9100000000-ea3054fa316845fc86b82021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Peroxisome
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
Tissue Locations
  • Epidermis
  • Fibroblasts
  • Intestine
  • Liver
  • Placenta
  • Skeletal Muscle
  • Spleen
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified89.0 +/- 28.0 uMAdult (>18 years old)BothNormal details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified62.0 +/- 28.0 uMAdult (>18 years old)Both
Short bowel syndrome
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer 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. [PubMed:15449570 ]
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB 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
Food Biomarker OntologyNot Available
VMH IDORN_D
MarkerDB IDNot Available
Good Scents IDNot Available
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. [PubMed:12948741 ]
  2. 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 ]
  3. Mayer UM: [Hyperornithinaemia in patients with retinal dystrophy]. Ophthalmologe. 2003 Jan;100(1):55-61. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed:11439164 ]
  16. 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. [PubMed:32033212 ]

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