Bovine Metabolome Database: Showing metabocard for D-Ornithine (BMDB0003374)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (3) Show 3 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:04:06 UTC

Update Date

2020-06-04 19:50:04 UTC

BMDB ID

BMDB0003374

Secondary Accession Numbers

BMDB03374

Metabolite Identification

Common Name

D-Ornithine

Description

D-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 possibly soluble (in water) and a very strong basic compound (based on its pKa). D-Ornithine can be converted into 5-amino-2-oxopentanoic acid through its interaction with the enzyme D-amino-acid oxidase. In cattle, D-ornithine is involved in the metabolic pathway called the D-arginine and D-ornithine metabolism pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

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

Chemical Formula

C₅H₁₂N₂O₂

Average Molecular Weight

132.161

Monoisotopic Molecular Weight

132.089877638

IUPAC Name

(2R)-2,5-diaminopentanoic acid

Traditional Name

L-(-)-ornithine

CAS Registry Number

348-66-3

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 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 )

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Peroxisome

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

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	13.74 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001u-9000000000-deb45bcb4280a1e67a8f	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0089-9300000000-bbfdea03043e52ad8a15	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00lr-3900000000-1b22374231fec22d1e20	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-9300000000-0ce9f8eaa9b98ad18d91	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-9000000000-45d863665ba8a53004f0	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-9000000000-b4769e364cb748464ebe	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-9000000000-aaadcea853770440853c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-1aeb351c8832822b88f7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-64dc476dd1cd337386ef	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9000000000-ef7c20aed1e9a71b1432	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-00di-9300000000-e36de55c16d7a2ed148f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-00xr-9700000000-a43025711954faa9935f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9000000000-1176f91c41c4400d1b5e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-f2bc6d43ca19a87e53ab	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-00xr-8900000000-03b469eaf5eacea319d6	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-00di-9000000000-09147e6ddaef03f93f15	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-001i-0900000000-0e3df57340c74126c5e7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-00b9-9000000000-d9ab801d36fbc1ca813f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-001i-3900000000-ae191a26241edfb2a693	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-00di-9400000000-9e4d5ca58ccec4283d21	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-00di-9000000000-8d64fc8fd06f41ed0f68	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-015i-7900000000-01f75740979c473383a0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00dr-9100000000-8f2f412b16c89d59e236	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00dl-9000000000-a216a8d4439f992b205b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-1900000000-59329678720e6407d762	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01qi-4900000000-8f53e4b8a940aa83cd3f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9000000000-5cfb47a9082ed47a2fa1	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Peroxisome

Biospecimen Locations

Epidermis
Fibroblasts
Intestine
Liver
Placenta
Skeletal Muscle
Spleen

Pathways

Name	SMPDB/Pathwhiz	KEGG
D-Arginine and D-Ornithine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Skeletal Muscle	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

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

References

Synthesis Reference

Furui, 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)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. D-aspartate oxidase

General function:: Amino acid transport and metabolism
Specific function:: Not Available
Gene Name:: DDO
Uniprot ID:: P31228
Molecular weight:: 37660.0

Reactions

D-Ornithine + Water + Oxygen → 5-Amino-2-oxopentanoic acid + Ammonia + Hydrogen peroxide	details

Enzyme Details

2. Ornithine decarboxylase antizyme 1

General function:: Involved in ornithine decarboxylase inhibitor activity
Specific function:: Ornithine decarboxylase (ODC) antizyme protein that negatively regulates ODC activity and intracellular polyamine biosynthesis and uptake in response to increased intracellular polyamine levels. Binds to ODC monomers, inhibiting the assembly of the functional ODC homodimer, and targets the monomers for ubiquitin-independent proteolytic destruction by the 26S proteasome. Triggers ODC degradation by inducing the exposure of a cryptic proteasome-interacting surface of ODC. Stabilizes AZIN2 by interfering with its ubiquitination. Also inhibits cellular uptake of polyamines by inactivating the polyamine uptake transporter. SMAD1/OAZ1/PSMB4 complex mediates the degradation of the CREBBP/EP300 repressor SNIP1. Involved in the translocation of AZIN2 from ER-Golgi intermediate compartment (ERGIC) to the cytosol.
Gene Name:: OAZ1
Uniprot ID:: Q56K12
Molecular weight:: 25448.0

Enzyme Details

3. Solute carrier family 25 (Mitochondrial carrier; ornithine transporter) member 15

General function:: Involved in binding
Specific function:: Not Available
Gene Name:: SLC25A15
Uniprot ID:: Q2KHW4
Molecular weight:: 32746.0

Showing metabocard for D-Ornithine (BMDB0003374)

Structure for BMDB0003374 (D-Ornithine)

Enzymes

Reactions