4BVH

CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Ex-527 Inhibits Sirtuins by Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism

Gertz, M., Fischer, F., Nguyen, G.T.T., Lakshminarasimhan, M., Schutkowski, M., Weyand, M., Steegborn, C.

(2013) Proc Natl Acad Sci U S A 110: E2772

  • DOI: 10.1073/pnas.1303628110
  • Primary Citation of Related Structures:  
    4BVB, 4BVE, 4BVF, 4BVG, 4BUZ, 4BV2, 4BV3, 4BVH

  • PubMed Abstract: 

    • Sirtuins are protein deacetylases regulating metabolism and stress responses. The seven human Sirtuins (Sirt1-7) are attractive drug targets, but Sirtuin inhibition mechanisms are mostly unidentified. We report the molecular mechanism of Sirtuin inhibition by 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide (Ex-527) ...

    Sirtuins are protein deacetylases regulating metabolism and stress responses. The seven human Sirtuins (Sirt1-7) are attractive drug targets, but Sirtuin inhibition mechanisms are mostly unidentified. We report the molecular mechanism of Sirtuin inhibition by 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide (Ex-527). Inhibitor binding to potently inhibited Sirt1 and Thermotoga maritima Sir2 and to moderately inhibited Sirt3 requires NAD(+), alone or together with acetylpeptide. Crystal structures of several Sirtuin inhibitor complexes show that Ex-527 occupies the nicotinamide site and a neighboring pocket and contacts the ribose of NAD(+) or of the coproduct 2'-O-acetyl-ADP ribose. Complex structures with native alkylimidate and thio-analog support its catalytic relevance and show, together with biochemical assays, that only the coproduct complex is relevant for inhibition by Ex-527, which stabilizes the closed enzyme conformation preventing product release. Ex-527 inhibition thus exploits Sirtuin catalysis, and kinetic isoform differences explain its selectivity. Our results provide insights in Sirtuin catalysis and inhibition with important implications for drug development.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIALA, B, C284Homo sapiensMutation(s): 0 
Gene Names: SIRT3, SIR2L3
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
NIH Common Fund Data Resources
PHAROS  Q9NTG7
GTEx  ENSG00000142082
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OAD
Query on OAD
Download Ideal Coordinates CCD File 
A, C
2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE
C17 H25 N5 O15 P2
BFNOPXRXIQJDHO-DLFWLGJNSA-N		 Ligand Interaction
AR6
Query on AR6
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
OCZ
Query on OCZ
Download Ideal Coordinates CCD File 
A, B, C
(1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide
C13 H13 Cl N2 O
FUZYTVDVLBBXDL-VIFPVBQESA-N		 Ligand Interaction
GOL
Query on GOL
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C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
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A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
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B, C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OCZIC50:  48700   nM  BindingDB
OCZIC50:  49000   nM  BindingDB
OCZIC50:  50000   nM  BindingDB
OCZIC50:  128000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.71α = 90
b = 66.53β = 90
c = 201.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references