Human Metabolome Database: Showing metabocard for N6-Acetyl-L-lysine (HMDB0000206)

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Record Information

Version

4.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2020-03-02 16:05:15 UTC

HMDB ID

HMDB0000206

Secondary Accession Numbers

HMDB00206

Metabolite Identification

Common Name

N6-Acetyl-L-lysine

Description

N6-Acetyl-L-lysine is an acetylated amino acid. Post-translational lysine-acetylation is one of two major modifications of lysine residues in various proteins. Acetylation of specific lysine residues in the N-terminal domains of core histones is a biochemical marker of active genes. Acetylation is now known to play a major role in eukaryotic transcription. Specifically, acetyltransferase enzymes that act on particular lysine side chains of histones and other proteins are intimately involved in transcriptional activation. By modifying chromatin proteins and transcription-related factors, these acetylases are believed to regulate the transcription of many genes. The best-characterized mechanism is acetylation, catalyzed by histone acetyltransferase (HAT) enzymes. HATs function enzymatically by transferring an acetyl group from acetyl-coenzyme A (acetyl-CoA) to the amino group of certain lysine side chains within a histone's basic N-terminal tail region. Within a histone octamer, these regions extend out from the associated globular domains, and in the context of a nucleosome, they are believed to bind the DNA through charge interactions (positively charged histone tails associated with negatively charged DNA) or mediate interactions between nucleosomes. Lysine acetylation, which neutralizes part of a tail region's positive charge, is postulated to weaken histone-DNA or nucleosome-nucleosome interactions and/or signal a conformational change, thereby destabilizing nucleosome structure or arrangement and giving other nuclear factors, such as the transcription complex, more access to a genetic locus. In agreement with this is the fact that acetylated chromatin has long been associated with states of transcriptional activation. Specific recognition of N-acetyl-L-lysine is a conserved function of all bromodomains found in different proteins, recognized as an emerging intracellular signalling mechanism that plays critical roles in regulating gene transcription, cell-cycle progression, apoptosis, DNA repair, and cytoskeletal organization (PMID: 9169194 , 10827952 , 17340003 , 16247734 , 9478947 , 10839822 ).

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
(2S)-6-(Acetylamino)-2-aminohexanoic acid	ChEBI
N(6)-ACETYLLYSINE	ChEBI
N(zeta)-Acetyllysine	ChEBI
N-epsilon-Acetyl-L-lysine	ChEBI
N-Epsilon-Acetyllysine	ChEBI
N(epsilon)-Acetyl-L-lysine	ChEBI
N(zeta)-Acetyl-L-lysine	ChEBI
(2S)-6-(Acetylamino)-2-aminohexanoate	Generator
N(Z)-Acetyllysine	Generator
N(Ζ)-acetyllysine	Generator
N(Z)-Acetyl-L-lysine	Generator
N(Ζ)-acetyl-L-lysine	Generator
e-Acetyl-L-lysine	HMDB
e-N-Acetyl-L-lysine	HMDB
e-N-Acetyllysine	HMDB
epsilon-Acetyl-L-lysine	HMDB
epsilon-N-Acetyl-L-lysine	HMDB
epsilon-N-Acetyllysine	HMDB
L-e-N-Acetyllysine	HMDB
L-epsilon-N-Acetyllysine	HMDB
N-e-Acetyl-L-lysine	HMDB
N-e-Acetyllysine	HMDB
N6-Acetyllysine	HMDB
Ne-acetyl-L-lysine	HMDB
Ne-acetyllysine	HMDB
Omega-N-acetyl-L-lysine	HMDB
W-N-Acetyl-L-lysine	HMDB
N(6)-Acetyllsine	HMDB
Omega-acetyllsine	HMDB
N6-Acetyl-L-lysine	ChEBI
(2S)-6-Acetamido-2-aminohexanoic acid	HMDB
6-Acetamido-2-aminohexanoic acid	HMDB
L-ε-N-Acetyllysine	HMDB
Nepsilon-Acetyl-L-lysine	HMDB
Nepsilon-Acetyllysine	HMDB
Nε-Acetyl-L-lysine	HMDB
Nε-Acetyllysine	HMDB
ε-Acetyl-L-lysine	HMDB
ε-N-Acetyl-L-lysine	HMDB
ε-N-Acetyllysine	HMDB
ω-N-Acetyl-L-lysine	HMDB

Chemical Formula

C₈H₁₆N₂O₃

Average Molecular Weight

188.2242

Monoisotopic Molecular Weight

188.116092388

IUPAC Name

(2S)-2-amino-6-acetamidohexanoic acid

Traditional Name

N6-acetyllysine

CAS Registry Number

692-04-6

SMILES

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

InChI Identifier

InChI=1S/C8H16N2O3/c1-6(11)10-5-3-2-4-7(9)8(12)13/h7H,2-5,9H2,1H3,(H,10,11)(H,12,13)/t7-/m0/s1

InChI Key

DTERQYGMUDWYAZ-ZETCQYMHSA-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

N(6)-acyl-L-lysine (CHEBI:17752 )
acetyl-L-lysine (CHEBI:17752 )

Ontology

Ingestion

Source:

Biological:

Animal

Plant:

Biological location:

Tissue and substructures:

Placenta

Subcellular:

Cytoplasm

Biofluid and excreta:

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	250 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	17.5 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-3.2	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	2.43	ChemAxon
pKa (Strongest Basic)	9.53	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	92.42 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	47.25 m³·mol⁻¹	ChemAxon
Polarizability	20.29 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	View
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0002-9610000000-6e30cfdb2a70cc49f983	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0002-9610000000-6e30cfdb2a70cc49f983	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-004i-1900000000-e36d5532f4f0ed8ec34f	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-9500000000-266c8b0fce84c71553b2	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-006x-9200000000-a186b34425c93ea31a66	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00di-9110000000-255e47c2dfcdf6b61403	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004r-1900000000-4745f7cfa9eaaef208ad	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-9000000000-635805826359aa05ec7c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-001i-9000000000-8857489c6ac957c71a5d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-000i-0900000000-39f91157038523017046	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-000j-0900000000-183e1f50c20603f14c03	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0002-1900000000-da02d0f8bd73b5b96b46	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0a4j-9400000000-8531cdbb4e8108dbec95	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0a4l-9000000000-94d72f2c644db8c0b5cd	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-000i-0900000000-c6ff005564503774a853	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-004i-3900000000-dffc604f608a010e711e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-001i-9000000000-d6bc330de42890c4c091	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-001i-9000000000-8d68337bf7a8db380cd7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-001i-9000000000-1400569a447d5f66c3a8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-000i-0900000000-39f91157038523017046	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-000j-0900000000-183e1f50c20603f14c03	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0002-1900000000-da02d0f8bd73b5b96b46	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4j-9400000000-8531cdbb4e8108dbec95	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4l-9000000000-94d72f2c644db8c0b5cd	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-000i-0900000000-c6ff005564503774a853	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0077-0900000000-e0d9659d3d504e9c8d81	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ued-3900000000-ae84e0c568d22d7c62fb	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9100000000-848f804e26f5a4edfcfb	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-545e3c760ee61913f301	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-05p2-3900000000-3a6e9f0c90d936bd6ae8	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9000000000-33c2ede158e490bcc70f	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Blood
Feces
Saliva
Urine

Tissue Locations

Placenta

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27065191	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	22308371	details
Urine	Detected and Quantified	2.036-2.828 umol/mmol creatinine	Adult (>18 years old)	Not Specified	Normal	6022933	details
Urine	Detected and Quantified	9.318 +/- 4.75 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	Mordechai, Hien, ...	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	27015276	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Attachment loss	31026179	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Periodontal Probing Depth	31026179	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Supragingival Plaque	31026179	details
Urine	Detected and Quantified	10.141 +/- 3.949 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	Mordechai, Hien, ...	details

Associated Disorders and Diseases

Disease References

Colorectal cancer
Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ] Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ] Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Attachment loss
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Periodontal Probing Depth
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Supragingival Plaque
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Eosinophilic esophagitis
(). Mordechai, Hien, and David S. Wishart. .

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB000476

KNApSAcK ID

Not Available

Chemspider ID

83801

KEGG Compound ID

C02727

BioCyc ID

CPD-567

BiGG ID

Not Available

Wikipedia Link

Acetyllysine

METLIN ID

5216

PubChem Compound

92832

PDB ID

Not Available

ChEBI ID

17752

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

References

Synthesis Reference

Benoiton, Leo; Leclerc, Jean. An improved synthesis of e-N-acetyl-L-lysine and similar compounds. Canadian Journal of Chemistry (1965), 43(4), 991-3.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Armstrong MD, Robinow M: A case of hyperlysinemia: biochemical and clinical observations. Pediatrics. 1967 Apr;39(4):546-54. [PubMed:6022933 ]
Crane-Robinson C, Hebbes TR, Clayton AL, Thorne AW: Chromosomal mapping of core histone acetylation by immunoselection. Methods. 1997 May;12(1):48-56. [PubMed:9169194 ]
Jacobson RH, Ladurner AG, King DS, Tjian R: Structure and function of a human TAFII250 double bromodomain module. Science. 2000 May 26;288(5470):1422-5. [PubMed:10827952 ]
Jamonnak N, Fatkins DG, Wei L, Zheng W: N(epsilon)-methanesulfonyl-lysine as a non-hydrolyzable functional surrogate for N(epsilon)-acetyl-lysine. Org Biomol Chem. 2007 Mar 21;5(6):892-6. Epub 2007 Feb 5. [PubMed:17340003 ]
Iwabata H, Yoshida M, Komatsu Y: Proteomic analysis of organ-specific post-translational lysine-acetylation and -methylation in mice by use of anti-acetyllysine and -methyllysine mouse monoclonal antibodies. Proteomics. 2005 Dec;5(18):4653-64. [PubMed:16247734 ]
Hazen SL, d'Avignon A, Anderson MM, Hsu FF, Heinecke JW: Human neutrophils employ the myeloperoxidase-hydrogen peroxide-chloride system to oxidize alpha-amino acids to a family of reactive aldehydes. Mechanistic studies identifying labile intermediates along the reaction pathway. J Biol Chem. 1998 Feb 27;273(9):4997-5005. [PubMed:9478947 ]
Sterner DE, Berger SL: Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev. 2000 Jun;64(2):435-59. [PubMed:10839822 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for N6-Acetyl-L-lysine (HMDB0000206)

Structure for HMDB0000206 (N6-Acetyl-L-lysine)