5MAR | pdb_00005mar

Structure of human SIRT2 in complex with 1,2,4-Oxadiazole inhibitor and ADP ribose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.173 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5MAR

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Development of 1,2,4-Oxadiazoles as Potent and Selective Inhibitors of the Human Deacetylase Sirtuin 2: Structure-Activity Relationship, X-ray Crystal Structure, and Anticancer Activity.

Moniot, S.Forgione, M.Lucidi, A.Hailu, G.S.Nebbioso, A.Carafa, V.Baratta, F.Altucci, L.Giacche, N.Passeri, D.Pellicciari, R.Mai, A.Steegborn, C.Rotili, D.

(2017) J Med Chem 60: 2344-2360

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01609
  • Primary Citation Related Structures: 
    5MAR

  • PubMed Abstract: 

    Sirt2 is a target for the treatment of neurological, metabolic, and age-related diseases including cancer. Here we report a series of Sirt2 inhibitors based on the 1,2,4-oxadiazole scaffold. These compounds are potent Sirt2 inhibitors active at single-digit μM level by using the Sirt2 substrate α-tubulin-acetylLys40 peptide and inactive up to 100 μM against Sirt1, -3, and -5 (deacetylase and desuccinylase activities). Their mechanism of inhibition is uncompetitive toward both the peptide substrate and NAD + , and the crystal structure of a 1,2,4-oxadiazole analog in complex with Sirt2 and ADP-ribose reveals its orientation in a still unexplored subcavity useful for further inhibitor development. Tested in leukemia cell lines, 35 and 39 induced apoptosis and/or showed antiproliferative effects at 10 or 25 μM after 48 h. Western blot analyses confirmed the involvement of Sirt2 inhibition for their effects in NB4 and in U937 cells. Our results provide novel Sirt2 inhibitors with a compact scaffold and structural insights for further inhibitor improvement.


  • Organizational Affiliation
    • Department of Biochemistry and Research Center for Bio-Macromolecules, University of Bayreuth , 95440 Bayreuth, Germany.

Macromolecule Content 

  • Total Structure Weight: 71.7 kDa 
  • Atom Count: 5,494 
  • Modeled Residue Count: 604 
  • Deposited Residue Count: 606 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-2
A, B
303Homo sapiensMutation(s): 0 
Gene Names: SIRT2SIR2LSIR2L2
EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
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

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AR6

Query on AR6



Download:Ideal Coordinates CCD File
D [auth A],
P [auth B]
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
7KE

Query on 7KE



Download:Ideal Coordinates CCD File
E [auth A],
Q [auth B]
3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]propan-1-ol
C11 H11 Cl N2 O2
BTURSBZSHDJVMU-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
W [auth B],
X [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
O [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
R [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.557α = 90
b = 76.709β = 90
c = 113.827γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alzheimer Forschung Initiative e.V.Germany14834

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Author supporting evidence, Data collection, Database references, Refinement description, Structure summary