5Y5N image
Deposition Date 2017-08-09
Release Date 2017-09-06
Last Version Date 2023-11-22
Entry Detail
PDB ID:
5Y5N
Title:
Crystal structure of human Sirtuin 2 in complex with a selective inhibitor
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.25
R-Value Work:
0.25
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NAD-dependent protein deacetylase sirtuin-2
Gene (Uniprot):SIRT2
Chain IDs:A
Chain Length:336
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Potent mechanism-based sirtuin-2-selective inhibition by anin situ-generated occupant of the substrate-binding site, "selectivity pocket" and NAD+-binding site.
Chem Sci 8 6400 6408 (2017)
PMID: 28989670 DOI: 10.1039/c7sc02738a

Abstact

Sirtuin 2 (SIRT2), a member of the NAD+-dependent histone deacetylase family, has recently received increasing attention due to its potential involvement in neurodegenerative diseases and the progression of cancer. Potent and selective SIRT2 inhibitors thus represent desirable biological probes. Based on the X-ray crystal structure of SIRT2 in complex with a previously reported weak inhibitor (6), we identified in this study the potent mechanism-based inactivator KPM-2 (36), which is selective toward SIRT2. Compound 36 engages in a nucleophilic attack toward NAD+ at the active site of SIRT2, which affords a stable 36-ADP-ribose conjugate that simultaneously occupies the substrate-binding site, the "selectivity pocket" and the NAD+-binding site. Moreover, 36 exhibits antiproliferative activity in cancer cells and remarkable neurite outgrowth activity. This strategy for the selective inhibition of SIRT2 should allow further probing of the biology of SIRT2, and promote the development of new disease treatment strategies.

Legend

Protein

Chemical

Disease

Primary Citation of related structures