5DY4 | pdb_00005dy4

Crystal structure of human Sirt2 in complex with a brominated 2nd generation SirReal inhibitor and NAD+

• PDB DOI: https://doi.org/10.2210/pdb5DY4/pdb

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


• Deposited: 2015-09-24 Released: 2016-01-13 
• 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: 1.77 Å
• R-Value Free: 
  0.213 (Depositor) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Aminothiazoles as Potent and Selective Sirt2 Inhibitors: A Structure-Activity Relationship Study.

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

(2016) J Med Chem 59: 1599-1612

• PubMed: 26696402 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01517
• Primary Citation Related Structures: 
  5DY4


• PubMed Abstract: 
  

  Sirtuins are NAD(+)-dependent protein deacylases that cleave off acetyl but also other acyl groups from the ε-amino group of lysines in histones and other substrate proteins. Dysregulation of human Sirt2 (hSirt2) activity has been associated with the pathogenesis of cancer, inflammation, and neurodegeneration, which makes the modulation of hSirt2 activity a promising strategy for pharmaceutical intervention. The sirtuin rearranging ligands (SirReals) have recently been discovered by us as highly potent and isotype-selective hSirt2 inhibitors. Here, we present a well-defined structure-activity relationship study, which rationalizes the unique features of the SirReals and probes the limits of modifications on this scaffold regarding inhibitor potency. Moreover, we present a crystal structure of hSirt2 in complex with an optimized SirReal derivative that exhibits an improved in vitro activity. Lastly, we show cellular hyperacetylation of the hSirt2 targeted tubulin caused by our improved lead structure.

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Organizational Affiliation: 
• Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg , Albertstraße 25, 79104 Freiburg im Breisgau, Germany.
Institute of Pharmacy, Martin-Luther-University 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 of Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg , Albertstraße 21, 79104 Freiburg im Breisgau, Germany.

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: 35.65 kDa 
• Atom Count: 2,649 
• Modeled Residue Count: 301 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
5GN	C [auth A]	N-{5-[(7-bromonaphthalen-1-yl)methyl]-1,3-thiazol-2-yl}-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide C22 H19 Br N4 O S2 YKVBPTQPNLFGIG-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5GN	BindingDB:  5DY4	IC50: 210 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.213 (Depositor) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.303	α = 90
b = 55.432	β = 114.91
c = 96.176	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-13 
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: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-01-20
  Changes: Database references
• Version 1.2: 2016-03-09
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Author supporting evidence, Data collection, Database references, Refinement description