MiMeDB: Showing metabocard for D-beta-lysine (MMDBc0054422)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:11:42 UTC

Update Date

2025-10-07 16:08:30 UTC

Metabolite ID

MMDBc0054422

Metabolite Identification

Common Name

D-beta-lysine

Description

D-beta-lysine is a non-proteinogenic amino acid belonging to the class of lysine derivatives. Its chemical structure features a beta-positioned amino group relative to the carboxyl group, distinguishing it from the more common L-lysine. D-beta-lysine can be synthesized through various biochemical pathways, notably involving the transformation of L-lysine via a newly identified 2,3-aminomutase, which facilitates its conversion from L-lysine, itself derived from acetates through the TCA cycle and the diaminopimelic acid pathway (PMID:1490884 ). Additionally, D-beta-lysine has been utilized as a precursor in synthetic chemistry, notably in the total synthesis of bellenamine through a modified CURTIUS reaction (PMID:1473996 ). Furthermore, it can be synthesized from D-ornithine via the ARNDT-EISTERT homologation sequence (PMID:1473996 ). The compound has also been isolated from culture conditions involving L-lysine and ammonium sulfate, highlighting its potential as a metabolic product in microbial systems (PMID:1490885 ). Overall, D-beta-lysine serves as an important compound in both synthetic and metabolic contexts within biochemical research.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
D-beta-Lysine	ChEBI
D-b-Lysine	Generator
D-Β-lysine	Generator
(3R)-3,6-Diaminohexanoate	Generator

Molecular Formula

C₆H₁₄N₂O₂

Average Mass

146.1876

Monoisotopic Mass

146.105527702

IUPAC Name

(3R)-3,6-diaminohexanoic acid

Traditional Name

(3R)-3,6-diaminohexanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](N)(CCCN)CC(O)=O

InChI Identifier

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

InChI Key

QKEWQOJCHPFEAF-RXMQYKEDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta 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

Beta amino acids and derivatives

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

beta-amino acid (CHEBI:85040 )
diamino acid (CHEBI:85040 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	99.3 g/L	ALOGPS
logP	-3.6	ALOGPS
logP	-3.7	ChemAxon
logS	-0.17	ALOGPS
pKa (Strongest Acidic)	4.25	ChemAxon
pKa (Strongest Basic)	10.71	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	5	ChemAxon
Refractivity	37.83 m³·mol⁻¹	ChemAxon
Polarizability	15.86 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_5) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01u1-0900000000-31a9427608c2c6cf8b04	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0239-9800000000-2298ec3453e0a5ff2031	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06sl-9100000000-f8bdfada6a643b679bd7	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0900000000-1f6f09131fc1c91f4093	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ufs-1900000000-7ea2e6358f53533dd216	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-053u-9200000000-a213880c5cc2d1a3977f	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 (eluted)	2025-10-24	505.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	440.2
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	38.1
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	224.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	278.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	258.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	348.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	949.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	548.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	157.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	717.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	170.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	47.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	427.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	983.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	54.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	245.0
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	536.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	529.4

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	D-beta-lysine_TMS_1	C[Si](C)(C)OC(=O)C[C@H](N)CCCN	standard non polar	2025-10-24	1445.46
Gas Chromatography	D-beta-lysine_TMS_2	C[Si](C)(C)N[C@H](CCCN)CC(=O)O	standard non polar	2025-10-24	2028.38
Gas Chromatography	D-beta-lysine_TMS_3	C[Si](C)(C)NCCC[C@@H](N)CC(=O)O	standard non polar	2025-10-24	1692.98
Gas Chromatography	D-beta-lysine_TMS_4	C[Si](C)(C)N[C@H](CCCN)CC(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1976.76
Gas Chromatography	D-beta-lysine_TMS_5	C[Si](C)(C)NCCC[C@@H](N)CC(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1683.44
Gas Chromatography	D-beta-lysine_TMS_6	C[Si](C)(C)NCCC[C@H](CC(=O)O)N[Si](C)(C)C	standard non polar	2025-10-24	1915.92
Gas Chromatography	D-beta-lysine_TMS_7	C[Si](C)(C)N([C@H](CCCN)CC(=O)O)[Si](C)(C)C	standard non polar	2025-10-24	2455.36
Gas Chromatography	D-beta-lysine_TMS_8	C[Si](C)(C)N(CCC[C@@H](N)CC(=O)O)[Si](C)(C)C	standard non polar	2025-10-24	1706.57
Gas Chromatography	D-beta-lysine_TMS_9	C[Si](C)(C)NCCC[C@H](CC(=O)O[Si](C)(C)C)N[Si](C)(C)C	standard non polar	2025-10-24	1571.44
Gas Chromatography	D-beta-lysine_TMS_10	C[Si](C)(C)OC(=O)C[C@@H](CCCN)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1836.1
Gas Chromatography	D-beta-lysine_TMS_11	C[Si](C)(C)OC(=O)C[C@H](N)CCCN([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1457.23
Gas Chromatography	D-beta-lysine_TMS_12	C[Si](C)(C)N[C@H](CCCN([Si](C)(C)C)[Si](C)(C)C)CC(=O)O	standard non polar	2025-10-24	2205.55
Gas Chromatography	D-beta-lysine_TMS_13	C[Si](C)(C)NCCC[C@H](CC(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1817.74
Gas Chromatography	D-beta-lysine_TMS_14	C[Si](C)(C)N[C@H](CCCN([Si](C)(C)C)[Si](C)(C)C)CC(=O)O[Si](C)(C)C	standard non polar	2025-10-24	951.0
Gas Chromatography	D-beta-lysine_TMS_15	C[Si](C)(C)NCCC[C@H](CC(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1889.43
Gas Chromatography	D-beta-lysine_TMS_16	C[Si](C)(C)N(CCC[C@H](CC(=O)O)N([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1651.51
Gas Chromatography	D-beta-lysine_TMS_17	C[Si](C)(C)OC(=O)C[C@@H](CCCN([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	2127.31
Gas Chromatography	D-beta-lysine_TMS_1	C[Si](C)(C)OC(=O)C[C@H](N)CCCN	standard polar	2025-10-24	2634.67
Gas Chromatography	D-beta-lysine_TMS_2	C[Si](C)(C)N[C@H](CCCN)CC(=O)O	standard polar	2025-10-24	2467.49
Gas Chromatography	D-beta-lysine_TMS_3	C[Si](C)(C)NCCC[C@@H](N)CC(=O)O	standard polar	2025-10-24	2053.7
Gas Chromatography	D-beta-lysine_TMS_4	C[Si](C)(C)N[C@H](CCCN)CC(=O)O[Si](C)(C)C	standard polar	2025-10-24	2219.63
Gas Chromatography	D-beta-lysine_TMS_5	C[Si](C)(C)NCCC[C@@H](N)CC(=O)O[Si](C)(C)C	standard polar	2025-10-24	2283.1
Gas Chromatography	D-beta-lysine_TMS_6	C[Si](C)(C)NCCC[C@H](CC(=O)O)N[Si](C)(C)C	standard polar	2025-10-24	1926.56
Gas Chromatography	D-beta-lysine_TMS_7	C[Si](C)(C)N([C@H](CCCN)CC(=O)O)[Si](C)(C)C	standard polar	2025-10-24	1918.64
Gas Chromatography	D-beta-lysine_TMS_8	C[Si](C)(C)N(CCC[C@@H](N)CC(=O)O)[Si](C)(C)C	standard polar	2025-10-24	1874.75
Gas Chromatography	D-beta-lysine_TMS_9	C[Si](C)(C)NCCC[C@H](CC(=O)O[Si](C)(C)C)N[Si](C)(C)C	standard polar	2025-10-24	2640.75
Gas Chromatography	D-beta-lysine_TMS_10	C[Si](C)(C)OC(=O)C[C@@H](CCCN)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1685.63
Gas Chromatography	D-beta-lysine_TMS_11	C[Si](C)(C)OC(=O)C[C@H](N)CCCN([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2228.72
Gas Chromatography	D-beta-lysine_TMS_12	C[Si](C)(C)N[C@H](CCCN([Si](C)(C)C)[Si](C)(C)C)CC(=O)O	standard polar	2025-10-24	2194.29
Gas Chromatography	D-beta-lysine_TMS_13	C[Si](C)(C)NCCC[C@H](CC(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2075.3
Gas Chromatography	D-beta-lysine_TMS_14	C[Si](C)(C)N[C@H](CCCN([Si](C)(C)C)[Si](C)(C)C)CC(=O)O[Si](C)(C)C	standard polar	2025-10-24	1918.3
Gas Chromatography	D-beta-lysine_TMS_15	C[Si](C)(C)NCCC[C@H](CC(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2079.14
Gas Chromatography	D-beta-lysine_TMS_16	C[Si](C)(C)N(CCC[C@H](CC(=O)O)N([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2046.15
Gas Chromatography	D-beta-lysine_TMS_17	C[Si](C)(C)OC(=O)C[C@@H](CCCN([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2387.03

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	4	Human
Bacteria	Proteobacteria	1	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

Not Available

BioCyc ID

CPD0-1032

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10931575

PDB ID

Not Available

ChEBI ID

85040

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 D-beta-lysine (MMDBc0054422)

MOL for #<Metabolite:0x00007f9af10c4818>

3D MOL for #<Metabolite:0x00007f9af10c4818>

3D SDF for #<Metabolite:0x00007f9af10c4818>

3D-SDF for #<Metabolite:0x00007f9af10c4818>

PDB for #<Metabolite:0x00007f9af10c4818>

3D PDB for #<Metabolite:0x00007f9af10c4818>

SMILES for #<Metabolite:0x00007f9af10c4818>

INCHI for #<Metabolite:0x00007f9af10c4818>

Structure for #<Metabolite:0x00007f9af10c4818>

3D Structure for #<Metabolite:0x00007f9af10c4818>