MiMeDB: Showing metabocard for N(5)-hydroxy-L-ornithine (MMDBc0054597)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:20:17 UTC

Update Date

2025-10-07 16:08:35 UTC

Metabolite ID

MMDBc0054597

Metabolite Identification

Common Name

N(5)-hydroxy-L-ornithine

Description

N(5)-hydroxy-L-ornithine is a member of the amino acid class, specifically a hydroxylated derivative of L-ornithine. Its chemical structure features a hydroxyl group attached to the nitrogen at the N(5) position of the ornithine backbone, which is a key component in various metabolic pathways. This metabolite is synthesized through the action of the flavoprotein VbsO, which functions as an l-ornithine N(5)-hydroxylase, initiating the hydroxylation process. Subsequently, the enzyme VbsA catalyzes the transfer of (R)-3-hydroxybutyryl from a CoA thioester to N(5)-hydroxyornithine, resulting in the formation of N(5)-((R)-3-hydroxybutyryl)-N(5)-hydroxy-L-ornithine. This compound is involved in the biosynthetic pathways of certain natural products, contributing to the chemical diversity of secondary metabolites in various organisms. The enzymatic processes that produce N(5)-hydroxy-L-ornithine highlight its role in the intricate network of amino acid metabolism and its potential implications in biochemical research. (PMID:19778043 )

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
N(5)-Hydroxy-L-ornithine	ChEBI
DL-2-amino-5-Hydroxylaminopentanoic acid	MeSH
delta-N-Hydroxyornithine	MeSH
Omega-N-hydroxyornithine	MeSH

Molecular Formula

C₅H₁₂N₂O₃

Average Mass

148.1604

Monoisotopic Mass

148.08479226

IUPAC Name

(2S)-2-amino-5-(hydroxyamino)pentanoic acid

Traditional Name

(2S)-2-amino-5-(hydroxyamino)pentanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@](N)(CCCNO)C(O)=O

InChI Identifier

InChI=1S/C5H12N2O3/c6-4(5(8)9)2-1-3-7-10/h4,7,10H,1-3,6H2,(H,8,9)/t4-/m0/s1

InChI Key

OZMJDTPATROLQC-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
N-organohydroxylamine
Monocarboxylic acid or derivatives
Carboxylic acid
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Organic nitrogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Organopnictogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

hydroxylamines (CHEBI:79095 )
non-proteinogenic alpha-amino acid (CHEBI:79095 )
L-ornithine derivative (CHEBI:79095 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	117 g/L	ALOGPS
logP	-3.1	ALOGPS
logP	-3.3	ChemAxon
logS	-0.1	ALOGPS
pKa (Strongest Acidic)	2.35	ChemAxon
pKa (Strongest Basic)	9.53	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	95.58 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	45.47 m³·mol⁻¹	ChemAxon
Polarizability	14.82 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	504.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	402.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	39.0
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	226.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	281.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	289.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	395.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	858.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (retained)	2025-10-24	626.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	167.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	578.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	175.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	48.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	397.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	869.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	53.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	249.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	622.9
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	574.1

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_1	C[Si](C)(C)OC(=O)[C@@H](N)CCCNO	standard non polar	2025-10-24	1937.82
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_2	C[Si](C)(C)N[C@@H](CCCNO)C(=O)O	standard non polar	2025-10-24	2124.42
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_3	C[Si](C)(C)N(O)CCC[C@H](N)C(=O)O	standard non polar	2025-10-24	1901.52
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_4	C[Si](C)(C)N[C@@H](CCCNO)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1624.78
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_5	C[Si](C)(C)OC(=O)[C@@H](N)CCCN(O)[Si](C)(C)C	standard non polar	2025-10-24	2520.48
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_6	C[Si](C)(C)N([C@@H](CCCNO)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-24	2015.71
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_7	C[Si](C)(C)N[C@@H](CCCN(O)[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	1748.64
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_8	C[Si](C)(C)OC(=O)[C@H](CCCNO)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	2103.07
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_9	C[Si](C)(C)N[C@@H](CCCN(O)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1772.58
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_10	C[Si](C)(C)N(O)CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1871.84
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_11	C[Si](C)(C)OC(=O)[C@H](CCCN(O)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1922.77
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_1	C[Si](C)(C)OC(=O)[C@@H](N)CCCNO	standard polar	2025-10-24	2158.77
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_2	C[Si](C)(C)N[C@@H](CCCNO)C(=O)O	standard polar	2025-10-24	1688.26
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_3	C[Si](C)(C)N(O)CCC[C@H](N)C(=O)O	standard polar	2025-10-24	1823.7
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_4	C[Si](C)(C)N[C@@H](CCCNO)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1442.09
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_5	C[Si](C)(C)OC(=O)[C@@H](N)CCCN(O)[Si](C)(C)C	standard polar	2025-10-24	1854.1
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_6	C[Si](C)(C)N([C@@H](CCCNO)C(=O)O)[Si](C)(C)C	standard polar	2025-10-24	1886.3
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_7	C[Si](C)(C)N[C@@H](CCCN(O)[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2568.6
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_8	C[Si](C)(C)OC(=O)[C@H](CCCNO)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1934.3
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_9	C[Si](C)(C)N[C@@H](CCCN(O)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2267.63
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_10	C[Si](C)(C)N(O)CCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2314.99
Gas Chromatography	N(5)-hydroxy-L-ornithine_TMS_11	C[Si](C)(C)OC(=O)[C@H](CCCN(O)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1750.51

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites
Eukaryota/Fungi	Basidiomycota	4
Bacteria/Eubacteria	Proteobacteria	2	Human ; Human subgingival plaque
Eukaryota/Fungi	Ascomycota	8

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

CPD-11571

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

169671

PDB ID

Not Available

ChEBI ID

78275

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for N(5)-hydroxy-L-ornithine (MMDBc0054597)

MOL for #<Metabolite:0x00007f2de71a9b60>

3D MOL for #<Metabolite:0x00007f2de71a9b60>

3D SDF for #<Metabolite:0x00007f2de71a9b60>

3D-SDF for #<Metabolite:0x00007f2de71a9b60>

PDB for #<Metabolite:0x00007f2de71a9b60>

3D PDB for #<Metabolite:0x00007f2de71a9b60>

SMILES for #<Metabolite:0x00007f2de71a9b60>

INCHI for #<Metabolite:0x00007f2de71a9b60>

Structure for #<Metabolite:0x00007f2de71a9b60>

3D Structure for #<Metabolite:0x00007f2de71a9b60>