4ZZI

SIRT1/Activator/Inhibitor Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7346 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic structure of a small molecule SIRT1 activator-enzyme complex.

Dai, H.Case, A.W.Riera, T.V.Considine, T.Lee, J.E.Hamuro, Y.Zhao, H.Jiang, Y.Sweitzer, S.M.Pietrak, B.Schwartz, B.Blum, C.A.Disch, J.S.Caldwell, R.Szczepankiewicz, B.Oalmann, C.Yee Ng, P.White, B.H.Casaubon, R.Narayan, R.Koppetsch, K.Bourbonais, F.Wu, B.Wang, J.Qian, D.Jiang, F.Mao, C.Wang, M.Hu, E.Wu, J.C.Perni, R.B.Vlasuk, G.P.Ellis, J.L.

(2015) Nat Commun 6: 7645-7645

  • DOI: 10.1038/ncomms8645
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SIRT1, the founding member of the mammalian family of seven NAD(+)-dependent sirtuins, is composed of 747 amino acids forming a catalytic domain and extended N- and C-terminal regions. We report the design and characterization of an engineered human ...

    SIRT1, the founding member of the mammalian family of seven NAD(+)-dependent sirtuins, is composed of 747 amino acids forming a catalytic domain and extended N- and C-terminal regions. We report the design and characterization of an engineered human SIRT1 construct (mini-hSIRT1) containing the minimal structural elements required for lysine deacetylation and catalytic activation by small molecule sirtuin-activating compounds (STACs). Using this construct, we solved the crystal structure of a mini-hSIRT1-STAC complex, which revealed the STAC-binding site within the N-terminal domain of hSIRT1. Together with hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis using full-length hSIRT1, these data establish a specific STAC-binding site and identify key intermolecular interactions with hSIRT1. The determination of the interface governing the binding of STACs with human SIRT1 facilitates greater understanding of STAC activation of this enzyme, which holds significant promise as a therapeutic target for multiple human diseases.


    Organizational Affiliation

    1] Sirtris, a GlaxoSmithKline Company, 200 Technology Square, Suite 300, Cambridge, Massachusetts 02139, USA [2] GlaxoSmithKline, 1250S. Collegeville Road, Collegeville, Pennsylvania 19426, USA.,Viva Biotech, 334 Aidisheng Road, Zhangjiang High-tech Park, Shanghai 201203, China.,High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 350 Shushanhu Road, Hefei, Anhui Province 230031, China.,ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, USA.,GlaxoSmithKline, 1250S. Collegeville Road, Collegeville, Pennsylvania 19426, USA.,Sirtris, a GlaxoSmithKline Company, 200 Technology Square, Suite 300, Cambridge, Massachusetts 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-1
A
356Homo sapiensMutation(s): 0 
Gene 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
1NS
Query on 1NS

Download SDF File 
Download CCD File 
A
4-(4-{2-[(methylsulfonyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide
C15 H21 N5 O3 S2
BKOWIHMCGFRARN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
4TQ
Query on 4TQ

Download SDF File 
Download CCD File 
A
(3S)-1,3-dimethyl-N-[3-(1,3-oxazol-5-yl)phenyl]-6-[3-(trifluoromethyl)phenyl]-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide
C26 H22 F3 N5 O2
NWNBKQCPAUNKSG-INIZCTEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1NSIC50: 4.3 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7346 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 122.150α = 90.00
b = 122.150β = 90.00
c = 104.920γ = 120.00
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-05-22 
  • Released Date: 2015-07-15 
  • Deposition Author(s): Dai, H.

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Data collection