9S44 | pdb_00009s44

Human Histone Deacetylase SIRT2

• PDB DOI: https://doi.org/10.2210/pdb9S44/pdb

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


• Deposited: 2025-07-25 Released: 2025-08-20 
• Deposition Author(s): Wirawan, R., Frei, M., Heider, A., Papenkordt, N., Friedrich, F., Wein, T., Jung, M., Groll, M., Huber, E.M., Bracher, F.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.274 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Tailored SirReal-type inhibitors enhance SIRT2 inhibition through ligand stabilization and disruption of NAD + co-factor binding.

Wirawan, R., Frei, M., Heider, A., Papenkordt, N., Friedrich, F., Wein, T., Jung, M., Groll, M., Huber, E.M., Bracher, F.

(2025) RSC Med Chem 

• PubMed: 40919320 
• DOI: https://doi.org/10.1039/d5md00144g
• Primary Citation of Related Structures:  
  9S44, 9S46, 9S48


• PubMed Abstract: 
  

  Human sirtuin 2 (SIRT2) is an NAD ⁺ dependant enzyme that has been linked to the pathogenesis of various diseases, making it a promising target for pharmaceutical intervention. This study presents a systematic investigation on the inhibitory effects of SIRT2 inhibitors functionalized with diverse electrophilic functional groups. Guided by initial docking studies, we designed and synthesised 14 derivatives of two published potent lead structures 24a and SirReal2. The most potent and subtype selective SIRT2 inhibitor 29 (RW-78) exhibits an IC ₅₀ of 26 nM, which outperforms its lead structure 24a (IC ₅₀ = 79 nM) by a factor of 3. The increased potency of 29 is explained by halogen-π interactions with SIRT2 residues as visualized by X-ray crystallography. Furthermore, 29 interferes with NAD ⁺ binding, highlighting co-factor displacement as a valid strategy to inhibit SIRT2. Additionally, we showed cellular target engagement via NanoBRET assays in HEK293T cells (EC ₅₀ = 15 nM). Altogether our findings provide a deeper insight into the structure-activity relationships of these SirReal-type inhibitors and offer new avenues for optimisation of SIRT2 inhibitors.

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Organizational Affiliation: 
• Department of Pharmacy, Ludwig-Maximilians University Munich Butenandtstraße 5-13 81377 Munich Germany [e-mail].
Center for Protein Assemblies, Technical University of Munich Ernst-Otto-Fischer Straße 8 85748 Garching Germany.
Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg Albertstraße 25 79104 Freiburg im Breisgau Germany.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.24 kDa 
• Atom Count: 2,251 
• Modeled Residue Count: 279 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	A	302	Homo sapiens	Mutation(s): 0  Gene Names: SIRT2, SIR2L, SIR2L2 EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (PDB Primary Data)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.274 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.76	α = 90
b = 73.51	β = 95.26
c = 54.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Wirawan, R., Frei, M., Heider, A., Papenkordt, N., Friedrich, F., Wein, T., Jung, M., Groll, M., Huber, E.M., Bracher, F.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	503267011
German Research Foundation (DFG)	Germany	325871075 (SFB1309)

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release
  
• Version 1.1: 2025-08-27
  Changes: Database references
• Version 1.2: 2025-09-24
  Changes: Database references