MiMeDB: Showing metabocard for N(6)-hydroxy-L-lysine (MMDBc0054600)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:20:33 UTC

Update Date

2025-10-07 16:08:35 UTC

Metabolite ID

MMDBc0054600

Metabolite Identification

Common Name

N(6)-hydroxy-L-lysine

Description

N(6)-hydroxy-L-lysine is a non-proteinogenic amino acid belonging to the class of hydroxy amino acids. There is limited literature available on this metabolite, indicating that further research may be needed to fully understand its biological significance and potential roles in metabolism.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
N6-Hydroxy-L-lysine	ChEBI

Molecular Formula

C₆H₁₄N₂O₃

Average Mass

162.189

Monoisotopic Mass

162.100442319

IUPAC Name

(2S)-2-amino-6-(hydroxyamino)hexanoic acid

Traditional Name

N6-hydroxy-L-lysine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H14N2O3/c7-5(6(9)10)3-1-2-4-8-11/h5,8,11H,1-4,7H2,(H,9,10)/t5-/m0/s1

InChI Key

FZQOIMPLZAYIKU-YFKPBYRVSA-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
Medium-chain fatty acid
Amino fatty acid
Fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
N-organohydroxylamine
Amine
Hydrocarbon derivative
Organic oxide
Primary amine
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Primary aliphatic amine
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

hydroxy-L-lysine (CHEBI:16570 )
N-hydroxy amino acid (CHEBI:16570 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	56.4 g/L	ALOGPS
logP	-2.9	ALOGPS
logP	-2.9	ChemAxon
logS	-0.46	ALOGPS
pKa (Strongest Acidic)	2.45	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	6	ChemAxon
Refractivity	50.07 m³·mol⁻¹	ChemAxon
Polarizability	16.88 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	splash10-02u1-1900000000-3b7dfe606a1fb14cbd3f	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9700000000-91e0f97413bcb46e3a0f	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-2e1441a3cdbd27775cf0	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0900000000-906e18b0310c88d2a3a6	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03dl-3900000000-5572efffda22314c5cd7	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00dl-9100000000-25ea85eb6f5ad66a7295	2019-02-23	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 (retained)	2025-10-24	500.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	401.6
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	42.2
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	236.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	271.7
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	275.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	429.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	859.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (retained)	2025-10-24	509.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	155.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	566.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	169.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	56.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (retained)	2025-10-24	386.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	934.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	61.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	212.9
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	640.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	595.3

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_1	C[Si](C)(C)OC(=O)[C@@H](N)CCCCNO	standard non polar	2025-10-24	2021.7
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_2	C[Si](C)(C)N[C@@H](CCCCNO)C(=O)O	standard non polar	2025-10-24	2033.4
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_3	C[Si](C)(C)N(O)CCCC[C@H](N)C(=O)O	standard non polar	2025-10-24	2167.56
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_4	C[Si](C)(C)N[C@@H](CCCCNO)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1622.21
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_5	C[Si](C)(C)OC(=O)[C@@H](N)CCCCN(O)[Si](C)(C)C	standard non polar	2025-10-24	1719.47
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_6	C[Si](C)(C)N([C@@H](CCCCNO)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-24	1728.01
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_7	C[Si](C)(C)N[C@@H](CCCCN(O)[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	1843.83
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_8	C[Si](C)(C)OC(=O)[C@H](CCCCNO)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	2171.53
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_9	C[Si](C)(C)N[C@@H](CCCCN(O)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2062.28
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_10	C[Si](C)(C)N(O)CCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1648.49
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_11	C[Si](C)(C)OC(=O)[C@H](CCCCN(O)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1990.33
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_1	C[Si](C)(C)OC(=O)[C@@H](N)CCCCNO	standard polar	2025-10-24	2163.27
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_2	C[Si](C)(C)N[C@@H](CCCCNO)C(=O)O	standard polar	2025-10-24	2087.98
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_3	C[Si](C)(C)N(O)CCCC[C@H](N)C(=O)O	standard polar	2025-10-24	1935.56
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_4	C[Si](C)(C)N[C@@H](CCCCNO)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2105.01
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_5	C[Si](C)(C)OC(=O)[C@@H](N)CCCCN(O)[Si](C)(C)C	standard polar	2025-10-24	2468.98
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_6	C[Si](C)(C)N([C@@H](CCCCNO)C(=O)O)[Si](C)(C)C	standard polar	2025-10-24	1540.12
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_7	C[Si](C)(C)N[C@@H](CCCCN(O)[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	1867.63
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_8	C[Si](C)(C)OC(=O)[C@H](CCCCNO)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1956.95
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_9	C[Si](C)(C)N[C@@H](CCCCN(O)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2277.44
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_10	C[Si](C)(C)N(O)CCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2039.59
Gas Chromatography	N(6)-hydroxy-L-lysine_TMS_11	C[Si](C)(C)OC(=O)[C@H](CCCCN(O)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1830.41

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	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal
Bacteria/Eubacteria	Actinobacteria	5	Cattle ; Human

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

C01028

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439370

PDB ID

Not Available

ChEBI ID

16570

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(6)-hydroxy-L-lysine (MMDBc0054600)

MOL for #<Metabolite:0x00007f9a8ee125f0>

3D MOL for #<Metabolite:0x00007f9a8ee125f0>

3D SDF for #<Metabolite:0x00007f9a8ee125f0>

3D-SDF for #<Metabolite:0x00007f9a8ee125f0>

PDB for #<Metabolite:0x00007f9a8ee125f0>

3D PDB for #<Metabolite:0x00007f9a8ee125f0>

SMILES for #<Metabolite:0x00007f9a8ee125f0>

INCHI for #<Metabolite:0x00007f9a8ee125f0>

Structure for #<Metabolite:0x00007f9a8ee125f0>

3D Structure for #<Metabolite:0x00007f9a8ee125f0>