Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 38234.19 
• Atom Count: 2316 
• Residue Count: 336 
• Unique protein chains: 1

5Y5N

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

• DOI: 10.2210/pdb5Y5N/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2017-08-09 Released: 2017-09-06 
• Deposition Author(s): Mellini, P., Itoh, Y., Tsumoto, H., Li, Y., Suzuki, M., Tokuda, N., Kakizawa, T., Miura, Y., Takeuchi, J., Lahtela-Kakkonen, M., Suzuki, T.

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Experimental Data Snapshot

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

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
Molecule	Chains	Sequence Length	Organism	Details
NAD-dependent protein deacetylase sirtuin-2	A	336	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
8NO	A	2-[[3-(2-phenylethoxy)phenyl]amino]benzamide C21 H20 N2 O2 VVRUXFPJOVUDCV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 50.850	α = 90.00
b = 57.980	β = 90.00
c = 124.532	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data collection
CNX	refinement
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-08-09 
• Released Date: 2017-09-06 
• Deposition Author(s): Mellini, P., Itoh, Y., Tsumoto, H., Li, Y., Suzuki, M., Tokuda, N., Kakizawa, T., Miura, Y., Takeuchi, J., Lahtela-Kakkonen, M., Suzuki, T.

Revision History 

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