4ZZI

SIRT1/Activator/Inhibitor Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/ncomms8645
  • Primary Citation of Related Structures:  
    4ZZH, 4ZZI, 4ZZJ

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-1356Homo sapiensMutation(s): 0 
Gene Names: SIRT1SIR2L1
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 Q96EB6 (Homo sapiens)
Explore Q96EB6 
Go to UniProtKB:  Q96EB6
PHAROS:  Q96EB6
GTEx:  ENSG00000096717 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EB6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4TQ
Query on 4TQ

Download Ideal Coordinates CCD File 
B [auth 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
1NS
Query on 1NS

Download Ideal Coordinates CCD File 
C [auth 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1NS BindingDB:  4ZZI IC50: 4.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.15α = 90
b = 122.15β = 90
c = 104.92γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Data collection
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description