5Y5N

Crystal structure of human Sirtuin 2 in complex with a selective inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Potent Mechanism-Based Sirtuin-2-Selective Inhibition by an In-Situ-Generated Occupant of the "Selectivity Pocket", Substrate Binding Site, and NAD+ Binding Pocket

Mellini, P.Itoh, Y.Tsumoto, H.Li, Y.Suzuki, M.Tokuda, M.Kakizawa, T.Miura, Y.Takeuchi, J.Lahtela-Kakkonen, M.Suzuki, T.

(2017) CHEM SCI 8: 6400-6408


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-2
A
336Homo sapiensMutation(s): 0 
Gene Names: SIRT2 (SIR2L, SIR2L2)
EC: 3.5.1.-
Find proteins for Q8IXJ6 (Homo sapiens)
Go to Gene View: SIRT2
Go to UniProtKB:  Q8IXJ6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8NO
Query on 8NO

Download SDF File 
Download CCD File 
A
2-[[3-(2-phenylethoxy)phenyl]amino]benzamide
C21 H20 N2 O2
VVRUXFPJOVUDCV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.256 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.850α = 90.00
b = 57.980β = 90.00
c = 124.532γ = 90.00
Software Package:
Software NamePurpose
DENZOdata collection
CNXrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-06
    Type: Initial release