MiMeDB: Showing metabocard for D-Lysine (MMDBc0000240)

Microbial

Human

Pharmaceutical

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:40:59 UTC

Update Date

2024-10-15 19:02:33 UTC

Metabolite ID

MMDBc0000240

Metabolite Identification

Common Name

D-Lysine

Description

D-Lysine is an essential amino acid. It is often added to animal feed.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

Molecular Formula

C₆H₁₄N₂O₂

Average Mass

146.19

Monoisotopic Mass

146.105527699

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

923-27-3

SMILES

Not Available

InChI Identifier

InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m1/s1

InChI Key

KDXKERNSBIXSRK-RXMQYKEDSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Not Available

Spectra

Not Available

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)	2025-10-23	542.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	459.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	39.0
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	229.5
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	271.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	278.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	396.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	977.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (retained)	2025-10-23	539.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	165.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	714.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	171.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	45.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (retained)	2025-10-23	423.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	1049.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	64.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	252.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	563.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	575.8

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	D-Lysine_TMS_1	C[Si](C)(C)OC(=O)[C@H](N)CCCCN	standard non polar	2025-10-23	2161.34
Gas Chromatography	D-Lysine_TMS_2	C[Si](C)(C)NCCCC[C@@H](N)C(=O)O	standard non polar	2025-10-23	2048.09
Gas Chromatography	D-Lysine_TMS_3	C[Si](C)(C)N[C@H](CCCCN)C(=O)O	standard non polar	2025-10-23	2042.96
Gas Chromatography	D-Lysine_TMS_4	C[Si](C)(C)N[C@H](CCCCN)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	2151.64
Gas Chromatography	D-Lysine_TMS_5	C[Si](C)(C)NCCCC[C@@H](N)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1884.58
Gas Chromatography	D-Lysine_TMS_6	C[Si](C)(C)NCCCC[C@@H](N[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	2036.28
Gas Chromatography	D-Lysine_TMS_7	C[Si](C)(C)N(CCCC[C@@H](N)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-23	2033.71
Gas Chromatography	D-Lysine_TMS_8	C[Si](C)(C)N([C@H](CCCCN)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-23	1359.9
Gas Chromatography	D-Lysine_TMS_9	C[Si](C)(C)NCCCC[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1984.86
Gas Chromatography	D-Lysine_TMS_10	C[Si](C)(C)OC(=O)[C@@H](CCCCN)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1294.08
Gas Chromatography	D-Lysine_TMS_11	C[Si](C)(C)OC(=O)[C@H](N)CCCCN([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1645.54
Gas Chromatography	D-Lysine_TMS_12	C[Si](C)(C)N[C@H](CCCCN([Si](C)(C)C)[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	1291.65
Gas Chromatography	D-Lysine_TMS_13	C[Si](C)(C)NCCCC[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1942.54
Gas Chromatography	D-Lysine_TMS_14	C[Si](C)(C)N[C@H](CCCCN([Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	2640.8
Gas Chromatography	D-Lysine_TMS_15	C[Si](C)(C)NCCCC[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2100.49
Gas Chromatography	D-Lysine_TMS_16	C[Si](C)(C)N(CCCC[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2014.85
Gas Chromatography	D-Lysine_TMS_17	C[Si](C)(C)OC(=O)[C@@H](CCCCN([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2254.19
Gas Chromatography	D-Lysine_TMS_1	C[Si](C)(C)OC(=O)[C@H](N)CCCCN	standard polar	2025-10-23	2545.96
Gas Chromatography	D-Lysine_TMS_2	C[Si](C)(C)NCCCC[C@@H](N)C(=O)O	standard polar	2025-10-23	1947.02
Gas Chromatography	D-Lysine_TMS_3	C[Si](C)(C)N[C@H](CCCCN)C(=O)O	standard polar	2025-10-23	2231.23
Gas Chromatography	D-Lysine_TMS_4	C[Si](C)(C)N[C@H](CCCCN)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1780.98
Gas Chromatography	D-Lysine_TMS_5	C[Si](C)(C)NCCCC[C@@H](N)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2202.44
Gas Chromatography	D-Lysine_TMS_6	C[Si](C)(C)NCCCC[C@@H](N[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	2408.84
Gas Chromatography	D-Lysine_TMS_7	C[Si](C)(C)N(CCCC[C@@H](N)C(=O)O)[Si](C)(C)C	standard polar	2025-10-23	1946.81
Gas Chromatography	D-Lysine_TMS_8	C[Si](C)(C)N([C@H](CCCCN)C(=O)O)[Si](C)(C)C	standard polar	2025-10-23	1891.52
Gas Chromatography	D-Lysine_TMS_9	C[Si](C)(C)NCCCC[C@@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2223.31
Gas Chromatography	D-Lysine_TMS_10	C[Si](C)(C)OC(=O)[C@@H](CCCCN)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2015.88
Gas Chromatography	D-Lysine_TMS_11	C[Si](C)(C)OC(=O)[C@H](N)CCCCN([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2219.35
Gas Chromatography	D-Lysine_TMS_12	C[Si](C)(C)N[C@H](CCCCN([Si](C)(C)C)[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	1597.17
Gas Chromatography	D-Lysine_TMS_13	C[Si](C)(C)NCCCC[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2180.54
Gas Chromatography	D-Lysine_TMS_14	C[Si](C)(C)N[C@H](CCCCN([Si](C)(C)C)[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1696.74
Gas Chromatography	D-Lysine_TMS_15	C[Si](C)(C)NCCCC[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	411.241
Gas Chromatography	D-Lysine_TMS_16	C[Si](C)(C)N(CCCC[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	1392.53
Gas Chromatography	D-Lysine_TMS_17	C[Si](C)(C)OC(=O)[C@@H](CCCCN([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2394.05

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces
Neuron

Tissue Locations

Neuron

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
MMDBr0026127	L-Lysine	D-Lysine	Broad substrate specificity amino-acid racemase	Racemization	RHEA	34755880

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	Firmicutes	7	Human feces	Microbial culture
Bacteria/Eubacteria	Proteobacteria	11	Human ; Human feces	Microbial culture
Bacteria/Eubacteria	Actinobacteria	1		Microbial culture
Bacteria/Eubacteria	Fusobacteria	2	Human mucosa; Human supragingival plaque; Human ; Human urine; Human feces; Human saliva; Human subgingival plaque	Microbial culture
Bacteria/Eubacteria	Bacteroidetes	1	Human feces	Microbial culture
Bacteria/Eubacteria	Thermotogae	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Neuron	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified						Infant (0-1 year old)	Both	Normal	HMDB	22411374

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

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Wakisaka K, Arano Y, Uezono T, Akizawa H, Ono M, Kawai K, Ohomomo Y, Nakayama M, Saji H: A novel radioiodination reagent for protein radiopharmaceuticals with L-lysine as a plasma-stable metabolizable linkage to liberate m-iodohippuric acid after lysosomal proteolysis. J Med Chem. 1997 Aug 1;40(16):2643-52. doi: 10.1021/jm9606397. [PubMed:9258371 ]
Bross R, Ball RO, Pencharz PB: Development of a minimally invasive protocol for the determination of phenylalanine and lysine kinetics in humans during the fed state. J Nutr. 1998 Nov;128(11):1913-9. doi: 10.1093/jn/128.11.1913. [PubMed:9808642 ]
Darling PB, Bross R, Wykes LJ, Ball RO, Pencharz PB: Isotopic enrichment of amino acids in urine following oral infusions of L-[1-(13)C]phenylalanine and L-[1-(13)C]lysine in humans: confounding effect of D-[13C]amino acids. Metabolism. 1999 Jun;48(6):732-7. doi: 10.1016/s0026-0495(99)90172-5. [PubMed:10381147 ]
Hayman MW, Smith KH, Cameron NR, Przyborski SA: Growth of human stem cell-derived neurons on solid three-dimensional polymers. J Biochem Biophys Methods. 2005 Mar 31;62(3):231-40. doi: 10.1016/j.jbbm.2004.12.001. Epub 2004 Dec 30. [PubMed:15733583 ]

Showing metabocard for D-Lysine (MMDBc0000240)

MOL for #<Metabolite:0x00007f9af0a2fbd8>

3D MOL for #<Metabolite:0x00007f9af0a2fbd8>

3D SDF for #<Metabolite:0x00007f9af0a2fbd8>

3D-SDF for #<Metabolite:0x00007f9af0a2fbd8>

PDB for #<Metabolite:0x00007f9af0a2fbd8>

3D PDB for #<Metabolite:0x00007f9af0a2fbd8>

SMILES for #<Metabolite:0x00007f9af0a2fbd8>

INCHI for #<Metabolite:0x00007f9af0a2fbd8>

Structure for #<Metabolite:0x00007f9af0a2fbd8>

3D Structure for #<Metabolite:0x00007f9af0a2fbd8>