Milk Composition Database: Showing metabocard for Ornithine (BMDB0000214)

Identification Taxonomy Physical properties Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:26:50 UTC

Update Date

2020-06-04 20:49:03 UTC

MCDB ID

BMDB0000214

Secondary Accession Numbers

BMDB00214

Metabolite Identification

Common Name

Ornithine

Description

Ornithine, also known as (S)-ornithine, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. Ornithine is a drug which is used for nutritional supplementation, also for treating dietary shortage or imbalance. it has been claimed that ornithine improves athletic performance, has anabolic effects, has wound-healing effects, and is immuno-enhancing. Ornithine exists as a solid, possibly soluble (in water), and a very strong basic compound (based on its pKa) molecule. Ornithine exists in all living species, ranging from bacteria to humans. Ornithine participates in a number of enzymatic reactions, within cattle. In particular, Carbamoyl phosphate and ornithine can be converted into citrulline; which is mediated by the enzyme ornithine carbamoyltransferase, mitochondrial. In addition, Ornithine and urea can be biosynthesized from L-arginine; which is mediated by the enzyme arginase-1. In cattle, ornithine is involved in the metabolic pathway called the urea cycle pathway. Ornithine is a potentially toxic compound.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(S)-2,5-Diaminopentanoate	ChEBI
(S)-2,5-Diaminopentanoic acid	ChEBI
(S)-2,5-Diaminovaleric acid	ChEBI
(S)-alpha,delta-Diaminovaleric acid	ChEBI
(S)-Ornithine	ChEBI
(S)-2,5-Diaminovalerate	Generator
(S)-a,delta-Diaminovalerate	Generator
(S)-a,delta-Diaminovaleric acid	Generator
(S)-alpha,delta-Diaminovalerate	Generator
(S)-Α,δ-diaminovalerate	Generator
(S)-Α,δ-diaminovaleric acid	Generator
(S)-a,Δ-diaminovalerate	HMDB
(S)-a,Δ-diaminovaleric acid	HMDB
(+)-S-Ornithine	HMDB
(S)-a,D-Diaminovalerate	HMDB
(S)-a,D-Diaminovaleric acid	HMDB
5-Amino-L-norvaline	HMDB
L-(-)-Ornithine	HMDB
L-Ornithine	HMDB
2,5-Diaminopentanoic acid	HMDB
Ornithine dihydrochloride, (L)-isomer	HMDB
Ornithine hydrochloride, (D)-isomer	HMDB
Ornithine, (D)-isomer	HMDB
Ornithine, (L)-isomer	HMDB
2,5 Diaminopentanoic acid	HMDB
Ornithine monoacetate, (L)-isomer	HMDB
Ornithine monohydrochloride, (D)-isomer	HMDB
Ornithine monohydrochloride, (DL)-isomer	HMDB
Ornithine phosphate (1:1), (L)-isomer	HMDB
Ornithine sulfate (1:1), (L)-isomer	HMDB
Ornithine hydrochloride, (DL)-isomer	HMDB
Ornithine hydrochloride, (L)-isomer	HMDB
Ornithine monohydrobromide, (L)-isomer	HMDB
Ornithine, (DL)-isomer	HMDB

Chemical Formula

C₅H₁₂N₂O₂

Average Molecular Weight

132.161

Monoisotopic Molecular Weight

132.089877638

IUPAC Name

(2S)-2,5-diaminopentanoic acid

Traditional Name

ornithine

CAS Registry Number

3184-13-2

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

Description

belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-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

L-alpha-amino acids

Alternative Parents

Substituents

L-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

non-proteinogenic L-alpha-amino acid (CHEBI:15729 )
ornithine (CHEBI:15729 )
Other amino acids (C00077 )

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
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	13.85 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-0006-1920000000-b0357b8c9888abda7d80	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0006-0910000000-8aaa0faabf1429b90611	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)	splash10-00di-7910000000-5fa118444ceb45204aa3	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-006x-3910000000-f6d0c6492f2cab33a392	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-00dr-2900000000-77222ff2d0118d3d3b57	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-0006-1910000000-53c73c4fa3665c44d3b9	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-03di-1691000000-dc14976cfee86cc828b9	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-0006-0920000000-f65f61e4a3739eabb1d1	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0006-1920000000-b0357b8c9888abda7d80	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0006-0910000000-8aaa0faabf1429b90611	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-7910000000-5fa118444ceb45204aa3	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-006x-3910000000-f6d0c6492f2cab33a392	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00dr-2900000000-77222ff2d0118d3d3b57	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0006-1910000000-53c73c4fa3665c44d3b9	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-03di-1691000000-dc14976cfee86cc828b9	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0006-0900000000-f59681b9f46f1b738487	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0006-0900000000-3048477975b51ae176af	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00dr-2900000000-8d1a2cc0a88f7d9216e1	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-1900000000-bc40b76e8b03ef7a08f0	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001l-9000000000-50fe14c2cb68fd09e32f	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0089-9300000000-bbfdea03043e52ad8a15	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-01b9-6900000000-8fe592b77d2d8e4ae704	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-9000000000-462b84db532c33527580	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00di-9000000000-9c9c28d2e40d5eadacd2	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-001i-0900000000-e44e06092c06bb4791af	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-9000000000-4d6ccc429f5155b24654	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-0900000000-dcad699e8ed7e1b19860	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-001i-0900000000-7b130437d4e1ceea277b	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-001i-0900000000-0fae230bc6b21623a4bf	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-9000000000-5a350a8e7c607a8b9a60	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-0900000000-516054b6c2f3cd4a1d02	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-000i-0793321000-9fef988b5ce019f84642	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-03di-0900000000-a612df8df5f8ba1ff7f3	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-001i-0910000000-97fad20414656e2b7b93	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-01di-0490000000-1b137b937beb110d2e4b	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-001i-0900000000-e3fc95eb909e45d8e648	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-001i-1900000000-cdd9aac89a5a71814ff3	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-001r-9500000000-f1cc3eccf3f5ab734222	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-0159-0900000000-93ce7b142d1f82f17e95	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-00di-9200000000-186f270471bdec40f804	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-00di-9000000000-ebbdf0ab6d3180cba1a5	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00di-9000000000-207bcc826fb2238c2cc5	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-00di-9000000000-a2f9a950fb23a6b18857	2012-08-31	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01c9-9700000000-0364d35bb1a7c10a09c7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00dr-9100000000-9c4015733140885b4957	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00dl-9000000000-b32e7180e30a835008bb	2016-09-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	2012-12-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, H₂O, experimental)	Not Available	2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)	Not Available	2016-10-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, experimental)	Not Available	2021-10-10	View Spectrum
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)	Not Available	2012-12-04	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	2012-12-05	View Spectrum

Concentrations

Status	Value	Reference	Details
Detected but not Quantified	Not Applicable	PMID: 23497994	details
Detected but not Quantified	Not Applicable	PMID: 25087032	details
Detected and Quantified	2 - 15 uM	PMID: 20338431	details

External Links

HMDB ID

HMDB0000214

DrugBank ID

DB00129

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

6262

PDB ID

Not Available

ChEBI ID

15729

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

Klein MS, Almstetter MF, Schlamberger G, Nurnberger N, Dettmer K, Oefner PJ, Meyer HH, Wiedemann S, Gronwald W: Nuclear magnetic resonance and mass spectrometry-based milk metabolomics in dairy cows during early and late lactation. J Dairy Sci. 2010 Apr;93(4):1539-50. doi: 10.3168/jds.2009-2563. [PubMed:20338431 ]
Sundekilde UK, Gustavsson F, Poulsen NA, Glantz M, Paulsson M, Larsen LB, Bertram HC: Association between the bovine milk metabolome and rennet-induced coagulation properties of milk. J Dairy Sci. 2014 Oct;97(10):6076-84. doi: 10.3168/jds.2014-8304. Epub 2014 Jul 30. [PubMed:25087032 ]
Buitenhuis AJ, Sundekilde UK, Poulsen NA, Bertram HC, Larsen LB, Sorensen P: Estimation of genetic parameters and detection of quantitative trait loci for metabolites in Danish Holstein milk. J Dairy Sci. 2013 May;96(5):3285-95. doi: 10.3168/jds.2012-5914. Epub 2013 Mar 15. [PubMed:23497994 ]
Mung D, Li L: Development of Chemical Isotope Labeling LC-MS for Milk Metabolomics: Comprehensive and Quantitative Profiling of the Amine/Phenol Submetabolome. Anal Chem. 2017 Apr 18;89(8):4435-4443. doi: 10.1021/acs.analchem.6b03737. Epub 2017 Mar 28. [PubMed:28306241 ]

Showing metabocard for Ornithine (BMDB0000214)

Structure for BMDB0000214 (Ornithine)