MiMeDB: Showing metabocard for N6-Formyllysine (MMDBc0000752)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:54:12 UTC

Update Date

2025-10-07 16:04:14 UTC

Metabolite ID

MMDBc0000752

Metabolite Identification

Common Name

N6-Formyllysine

Description

N6-Formyllysine is a metabolite classified as an amino acid derivative. There is limited literature available on this compound, indicating that further research may be needed to fully understand its biological significance and potential implications in health and disease.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 04-APR-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-APR-19         0                                  
HETATM    1  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.619   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       8.621   4.977   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       1.953   2.667   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      -0.715   2.667   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    6                                                       
CONECT    4    2    9                                                       
CONECT    5    9   10                                                       
CONECT    6    3    7    8                                                  
CONECT    7    6   11   12                                                  
CONECT    8    6                                                            
CONECT    9    4    5                                                       
CONECT   10    5                                                            
CONECT   11    7                                                            
CONECT   12    7                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
N(epsilon)-Formyllysine	ChEBI
N(6)-Formyllysine	MeSH

Molecular Formula

C₇H₁₄N₂O₃

Average Mass

174.2

Monoisotopic Mass

174.100442319

IUPAC Name

(2S)-2-amino-6-[(hydroxymethylidene)amino]hexanoic acid

Traditional Name

(2S)-2-amino-6-[(hydroxymethylidene)amino]hexanoic acid

CAS Registry Number

Not Available

SMILES

N[C@@H](CCCCN=CO)C(O)=O

InChI Identifier

InChI=1S/C7H14N2O3/c8-6(7(11)12)3-1-2-4-9-5-10/h5-6H,1-4,8H2,(H,9,10)(H,11,12)/t6-/m0/s1

InChI Key

KLPJXDPPMSJWKI-LURJTMIESA-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
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Primary amine
Organooxygen compound
Organonitrogen compound
Carbonyl group
Primary aliphatic amine
Organic nitrogen compound
Organic oxygen compound
Amine
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

formamides (CHEBI:21884 )
non-proteinogenic L-alpha-amino acid (CHEBI:21884 )
N(6)-acyl-L-lysine (CHEBI:21884 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.99 g/L	ALOGPS
logP	-2.7	ALOGPS
logP	-5	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	-2.7	ChemAxon
pKa (Strongest Basic)	12.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	95.91 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	43.28 m³·mol⁻¹	ChemAxon
Polarizability	18.16 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
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	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)	2025-10-23	480.0
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	384.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	45.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	241.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	266.4
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	254.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	458.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	777.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (retained)	2025-10-23	479.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	150.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	469.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	166.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	61.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	337.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	796.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	65.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	179.7
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	719.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	582.4

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	N6-Formyllysine_TMS_1	C[Si](C)(C)OC=NCCCC[C@H](N)C(=O)O	standard non polar	2025-10-23	1560.0
Gas Chromatography	N6-Formyllysine_TMS_2	C[Si](C)(C)OC(=O)[C@@H](N)CCCCN=CO	standard non polar	2025-10-23	1636.66
Gas Chromatography	N6-Formyllysine_TMS_3	C[Si](C)(C)N[C@@H](CCCCN=CO)C(=O)O	standard non polar	2025-10-23	1673.63
Gas Chromatography	N6-Formyllysine_TMS_4	C[Si](C)(C)OC=NCCCC[C@H](N)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1380.54
Gas Chromatography	N6-Formyllysine_TMS_5	C[Si](C)(C)N[C@@H](CCCCN=CO[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	1470.42
Gas Chromatography	N6-Formyllysine_TMS_6	C[Si](C)(C)N[C@@H](CCCCN=CO)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	2136.36
Gas Chromatography	N6-Formyllysine_TMS_7	C[Si](C)(C)N([C@@H](CCCCN=CO)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-23	2042.03
Gas Chromatography	N6-Formyllysine_TMS_8	C[Si](C)(C)N[C@@H](CCCCN=CO[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	2435.33
Gas Chromatography	N6-Formyllysine_TMS_9	C[Si](C)(C)OC=NCCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1685.74
Gas Chromatography	N6-Formyllysine_TMS_10	C[Si](C)(C)OC(=O)[C@H](CCCCN=CO)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2141.66
Gas Chromatography	N6-Formyllysine_TMS_11	C[Si](C)(C)OC=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	1794.53
Gas Chromatography	N6-Formyllysine_TMS_1	C[Si](C)(C)OC=NCCCC[C@H](N)C(=O)O	standard polar	2025-10-23	1871.75
Gas Chromatography	N6-Formyllysine_TMS_2	C[Si](C)(C)OC(=O)[C@@H](N)CCCCN=CO	standard polar	2025-10-23	1837.77
Gas Chromatography	N6-Formyllysine_TMS_3	C[Si](C)(C)N[C@@H](CCCCN=CO)C(=O)O	standard polar	2025-10-23	1999.6
Gas Chromatography	N6-Formyllysine_TMS_4	C[Si](C)(C)OC=NCCCC[C@H](N)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2862.57
Gas Chromatography	N6-Formyllysine_TMS_5	C[Si](C)(C)N[C@@H](CCCCN=CO[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	2535.17
Gas Chromatography	N6-Formyllysine_TMS_6	C[Si](C)(C)N[C@@H](CCCCN=CO)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2379.81
Gas Chromatography	N6-Formyllysine_TMS_7	C[Si](C)(C)N([C@@H](CCCCN=CO)C(=O)O)[Si](C)(C)C	standard polar	2025-10-23	2281.66
Gas Chromatography	N6-Formyllysine_TMS_8	C[Si](C)(C)N[C@@H](CCCCN=CO[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1784.38
Gas Chromatography	N6-Formyllysine_TMS_9	C[Si](C)(C)OC=NCCCC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	1941.2
Gas Chromatography	N6-Formyllysine_TMS_10	C[Si](C)(C)OC(=O)[C@H](CCCCN=CO)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	1639.79
Gas Chromatography	N6-Formyllysine_TMS_11	C[Si](C)(C)OC=NCCCC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2746.03

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	Verrucomicrobia	1	Human feces; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Firmicutes	3	Human feces; Human urine; Human sputum	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Actinobacteria	1	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen

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

HMDB0240349

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

64085

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70923

PDB ID

Not Available

ChEBI ID

21884

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Showing metabocard for N6-Formyllysine (MMDBc0000752)

MOL for #<Metabolite:0x00007f9ad0589bf8>

3D MOL for #<Metabolite:0x00007f9ad0589bf8>

3D SDF for #<Metabolite:0x00007f9ad0589bf8>

3D-SDF for #<Metabolite:0x00007f9ad0589bf8>

PDB for #<Metabolite:0x00007f9ad0589bf8>

3D PDB for #<Metabolite:0x00007f9ad0589bf8>

SMILES for #<Metabolite:0x00007f9ad0589bf8>

INCHI for #<Metabolite:0x00007f9ad0589bf8>

Structure for #<Metabolite:0x00007f9ad0589bf8>

3D Structure for #<Metabolite:0x00007f9ad0589bf8>