5DY5 | pdb_00005dy5

Crystal structure of human Sirt2 in complex with a SirReal probe fragment

• PDB DOI: https://doi.org/10.2210/pdb5DY5/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-24 Released: 2016-01-20 
• Deposition Author(s): Rumpf, T., Gerhardt, S., Einsle, O., Jung, M.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.205 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Development of an Affinity Probe for Sirtuin 2.

Schiedel, M., Rumpf, T., Karaman, B., Lehotzky, A., Gerhardt, S., Ovadi, J., Sippl, W., Einsle, O., Jung, M.

(2016) Angew Chem Int Ed Engl 55: 2252-2256

• PubMed: 26748890 
• DOI: https://doi.org/10.1002/anie.201509843
• Primary Citation Related Structures: 
  5DY5


• PubMed Abstract: 
  

  Sirtuins are NAD(+)-dependent protein deacylases that cleave off acetyl groups, as well as other acyl groups, from the ɛ-amino group of lysines in histones and other substrate proteins. Dysregulation of human Sirt2 activity has been associated with the pathogenesis of cancer, inflammation, and neurodegeneration, thus making Sirt2 a promising target for pharmaceutical intervention. Here, based on a crystal structure of Sirt2 in complex with an optimized sirtuin rearranging ligand (SirReal) that shows improved potency, water solubility, and cellular efficacy, we present the development of the first Sirt2-selective affinity probe. A slow dissociation of the probe/enzyme complex offers new applications for SirReals, such as biophysical characterization, fragment-based screening, and affinity pull-down assays. This possibility makes the SirReal probe an important tool for studying sirtuin biology.

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Organizational Affiliation: 
• Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany.
Institute für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120, Halle, Saale, Germany.
Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H-1117, Budapest, Hungary.
Institute für Biochemie und BIOSS Centre for Biological, Signaling Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.43 kDa 
• Atom Count: 2,687 
• Modeled Residue Count: 300 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	A	304	Homo sapiens	Mutation(s): 0  Gene Names: SIRT2, SIR2L, SIR2L2 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 Q8IXJ6 (Homo sapiens) Explore Q8IXJ6  Go to UniProtKB:  Q8IXJ6
PHAROS:  Q8IXJ6 GTEx:  ENSG00000068903

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GR	C [auth A]	N-(5-{3-[(1-benzyl-1H-1,2,3-triazol-4-yl)methoxy]benzyl}-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide C28 H27 N7 O2 S2 YWLNYZXFIAFWSF-UHFFFAOYSA-N
EPE	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
BU3	F [auth A]	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5GR	BindingDB:  5DY5	IC50: min: 160, max: 1400 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.205 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.15	α = 90
b = 53.36	β = 114.01
c = 83.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Rumpf, T., Gerhardt, S., Einsle, O., Jung, M.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	Ju295/8-1

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-02-10
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Author supporting evidence, Data collection, Database references, Refinement description