4I5I

Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 2.5 angstrom crystal structure of the SIRT1 catalytic domain bound to nicotinamide adenine dinucleotide (NAD+) and an indole (EX527 analogue) reveals a novel mechanism of histone deacetylase inhibition.

Zhao, X.Allison, D.Condon, B.Zhang, F.Gheyi, T.Zhang, A.Ashok, S.Russell, M.MacEwan, I.Qian, Y.Jamison, J.A.Luz, J.G.

(2013) J.Med.Chem. 56: 963-969

  • DOI: 10.1021/jm301431y

  • PubMed Abstract: 
  • The sirtuin SIRT1 is a NAD(+)-dependent histone deacetylase, a Sir2 family member, and one of seven human sirtuins. Sirtuins are conserved from archaea to mammals and regulate transcription, genome stability, longevity, and metabolism. SIRT1 regulate ...

    The sirtuin SIRT1 is a NAD(+)-dependent histone deacetylase, a Sir2 family member, and one of seven human sirtuins. Sirtuins are conserved from archaea to mammals and regulate transcription, genome stability, longevity, and metabolism. SIRT1 regulates transcription via deacetylation of transcription factors such as PPARγ, NFκB, and the tumor suppressor protein p53. EX527 (27) is a nanomolar SIRT1 inhibitor and a micromolar SIRT2 inhibitor. To elucidate the mechanism of SIRT inhibition by 27, we determined the 2.5 Å crystal structure of the SIRT1 catalytic domain (residues 241-516) bound to NAD(+) and the 27 analogue compound 35. 35 binds deep in the catalytic cleft, displacing the NAD(+) nicotinamide and forcing the cofactor into an extended conformation. The extended NAD(+) conformation sterically prevents substrate binding. The SIRT1/NAD(+)/35 crystal structure defines a novel mechanism of histone deacetylase inhibition and provides a basis for understanding, and rationally improving, inhibition of this therapeutically important target by drug-like molecules.


    Organizational Affiliation

    Lilly Biotechnology Center San Diego, 10300 Campus Point Drive, Suite 200, San Diego, California 92121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-1
A, B
287Homo sapiensGene Names: SIRT1 (SIR2L1)
EC: 3.5.1.-
Find proteins for Q96EB6 (Homo sapiens)
Go to Gene View: SIRT1
Go to UniProtKB:  Q96EB6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
4I5
Query on 4I5

Download SDF File 
Download CCD File 
A, B
(6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole-6-carboxamide
C14 H15 Cl N2 O
ABIVOOWWGYJNLV-JTQLQIEISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4I5IC50: 63 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 106.513α = 90.00
b = 106.513β = 90.00
c = 80.663γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Structure summary