MiMeDB: Showing metabocard for D-ornithine (MMDBc0054439)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:12:21 UTC

Update Date

2024-04-30 20:53:03 UTC

Metabolite ID

MMDBc0054439

Metabolite Identification

Common Name

D-ornithine

Description

D-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. D-Ornithine has been identified in the human placenta (PMID: 32033212 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

Synonyms

Value	Source
(R)-Ornithine	ChEBI
(2R)-2,5-Diaminopentanoate	HMDB
(2R)-2,5-Diaminopentanoic acid	HMDB
Ornithine	HMDB

Molecular Formula

C₅H₁₂N₂O₂

Average Mass

132.161

Monoisotopic Mass

132.089877638

IUPAC Name

(2R)-2,5-diaminopentanoic acid

Traditional Name

L-(-)-ornithine

CAS Registry Number

Not Available

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 Key

AHLPHDHHMVZTML-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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-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 Framework

Aliphatic acyclic compounds

External Descriptors

D-alpha-amino acid (CHEBI:16176 )
ornithine (CHEBI:16176 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	172 g/L	ALOGPS
logP	-3.6	ALOGPS
logP	-3.7	ChemAxon
logS	0.11	ALOGPS
pKa (Strongest Acidic)	2.67	ChemAxon
pKa (Strongest Basic)	10.29	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	89.34 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	33.21 m³·mol⁻¹	ChemAxon
Polarizability	13.74 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Peroxisome

Biospecimen Locations

Blood
Epidermis
Fibroblasts
Intestine
Liver
Placenta
Saliva
Skeletal Muscle
Spleen

Tissue Locations

Epidermis
Fibroblasts
Intestine
Liver
Placenta
Skeletal Muscle
Spleen

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191877	D-amino-acid oxidase	Unknown	P14920	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Short bowel syndrome	Slight Decrease	Association	Human Blood	HMDB	15449570

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites
Bacteria/Eubacteria	Firmicutes	4	Human feces; Human
Bacteria/Eubacteria	Thermotogae	1
Bacteria	Proteobacteria	1	Human
Bacteria/Eubacteria	Proteobacteria	2	Human
Bacteria	Actinobacteria	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Units	Age	Sex	Health Condition	Data Source	Reference
Human Blood	Detected and Quantified	62.0	28.0	uM	Adult (>18 years old)	Both	Short bowel syndrome	HMDB	15449570
Human Blood	Detected and Quantified	89.0	28.0	uM	Adult (>18 years old)	Both	Normal	HMDB	15449570
Human Epidermis	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597
Human Fibroblasts	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597
Human Intestine	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597
Human Skeletal muscle	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597
Human Spleen	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified				Adult (>18 years old)	Male	Normal	HMDB	22308371

External Links

HMDB ID

HMDB0003374

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023157

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

16176

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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. doi: 10.1023/a:1005397329395. [PubMed:9266387 ]
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. doi: 10.1089/hum.1997.8.17-2125. [PubMed:9414260 ]
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. doi: 10.1038/sj.ejhg.5200236. [PubMed:9887380 ]
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 ]
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. doi: 10.1067/mlc.2001.114543. [PubMed:11329531 ]
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 ]
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 ]
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. doi: 10.1046/j.1365-3083.2001.00936.x. [PubMed:11439164 ]
Mayer UM: [Hyperornithinaemia in patients with retinal dystrophy]. Ophthalmologe. 2003 Jan;100(1):55-61. doi: 10.1007/s00347-002-0657-2. [PubMed:12557027 ]
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. doi: 10.1016/s1096-7192(03)00105-7. [PubMed:12948741 ]
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. doi: 10.1097/00075197-200501000-00007. [PubMed:15585999 ]
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. doi: 10.1196/annals.1333.015. [PubMed:16037230 ]
Monnier VM, Sell DR: Prevention and repair of protein damage by the Maillard reaction in vivo. Rejuvenation Res. 2006 Summer;9(2):264-73. doi: 10.1089/rej.2006.9.264. [PubMed:16706654 ]
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. doi: 10.1016/j.ymgme.2006.04.007. Epub 2006 Jun 5. [PubMed:16753325 ]
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. doi: 10.1016/s0261-5614(97)80015-5. [PubMed:16844612 ]
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 ]

Showing metabocard for D-ornithine (MMDBc0054439)

MOL for #<Metabolite:0x00007f9238178fa0>

3D MOL for #<Metabolite:0x00007f9238178fa0>

3D SDF for #<Metabolite:0x00007f9238178fa0>

3D-SDF for #<Metabolite:0x00007f9238178fa0>

PDB for #<Metabolite:0x00007f9238178fa0>

3D PDB for #<Metabolite:0x00007f9238178fa0>

SMILES for #<Metabolite:0x00007f9238178fa0>

INCHI for #<Metabolite:0x00007f9238178fa0>

Structure for #<Metabolite:0x00007f9238178fa0>

3D Structure for #<Metabolite:0x00007f9238178fa0>