5YQL

Crystal structure of Sirt2 in complex with selective inhibitor A2I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

X-ray crystal structure guided discovery of new selective, substrate-mimicking sirtuin 2 inhibitors that exhibit activities against non-small cell lung cancer cells.

Yang, L.L.Wang, H.L.Zhong, L.Yuan, C.Liu, S.Y.Yu, Z.J.Liu, S.Yan, Y.H.Wu, C.Wang, Y.Wang, Z.Yu, Y.Chen, Q.Li, G.B.

(2018) Eur J Med Chem 155: 806-823

  • DOI: https://doi.org/10.1016/j.ejmech.2018.06.041
  • Primary Citation of Related Structures:  
    5YQL, 5YQM, 5YQN, 5YQO

  • PubMed Abstract: 

    Human sirtuin 2 (SIRT2) is a nicotinamide adenine dinucleotide (NAD + )-dependent deacylase, and is implicated in human diseases including cancer. Selective small-molecule inhibitors for SIRT2 are sought as chemical tools and potential therapeutics. Here we report the X-ray crystal structure guided structure-activity relationship studies of new N-(3-(phenoxymethyl)phenyl)acetamide derivatives with SIRT2, which led to the identification of potent, selective SIRT2 inhibitors. Crystallographic analyses reveal that the new inhibitors act via inducing the formation of an enlarged hydrophobic pocket and particularly mimicking the interactions made by myristoylated-lysine substrates. The most potent inhibitor 24a could dose-dependently elevate the acetylation level of α-tubulin in the non-small cell lung cancer H441 cells, which have a high expression level of SIRT2 as determinated by Western blotting analyses. Further cellular assays reveal that 24a restrains cell growth mainly through inhibiting cellular proliferation rather than inducing apoptosis. Moreover, 24a could suppress the migration and invasion of H441 cells. These results provide an excellent basis for further development of new potent, selective, and cell active SIRT2 inhibitors as chemical tools and potential therapeutics for SIRT2-driven non-small cell lung cancers.


  • Organizational Affiliation

    Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, China; College of Food and Bioengineering, Xihua University, Sichuan, 610039, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-2306Homo sapiensMutation(s): 0 
Gene Names: SIRT2SIR2LSIR2L2
EC: 3.5.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXJ6 (Homo sapiens)
Explore Q8IXJ6 
Go to UniProtKB:  Q8IXJ6
PHAROS:  Q8IXJ6
GTEx:  ENSG00000068903 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IXJ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
A2I Binding MOAD:  5YQL IC50: 2.59e+4 (nM) from 1 assay(s)
BindingDB:  5YQL IC50: min: 2.59e+4, max: 2.63e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.038α = 90
b = 73.95β = 95.11
c = 55.797γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description