Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.65 kDa 
• Atom Count: 7157 
• Modelled Residue Count: 813 
• Deposited Residue Count: 852 
• Unique protein chains: 1

4BVH

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

• PDB DOI: 10.2210/pdb4BVH/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-25 Released: 2013-07-17 
• Deposition Author(s): Gertz, M., Weyand, M., Steegborn, C.

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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 

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

• PubMed: 23840057 
• DOI: 10.1073/pnas.1303628110
• Primary Citation of Related Structures:  
  4BUZ, 4BV2, 4BV3, 4BVB, 4BVE, 4BVF, 4BVG, 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). 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL	A, B, C	284	Homo sapiens	Mutation(s): 0  Gene Names: SIRT3, SIR2L3 EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7  Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OAD	E [auth A], P [auth C]	2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE C17 H25 N5 O15 P2 BFNOPXRXIQJDHO-DLFWLGJNSA-N
AR6	J [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
OCZ	D [auth A], I [auth B], O [auth C]	(1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide C13 H13 Cl N2 O FUZYTVDVLBBXDL-VIFPVBQESA-N
GOL	R [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	F [auth A], M [auth B], U [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	K [auth B], L [auth B], Q [auth C], S [auth C], T [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	H [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OCZ	BindingDB:  4BVH	IC50: min: 2.54e+4, max: 1.28e+5 (nM) from 6 assay(s)

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 = 63.71	α = 90
b = 66.53	β = 90
c = 201.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-25 
• Released Date: 2013-07-17 
Deposition Author(s): Gertz, M., Weyand, M., Steegborn, C.

Revision History  

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