9IM8 | pdb_00009im8

Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9IM8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-07-02 Released: 2025-07-09 
• Deposition Author(s): Wang, X.Y., Tian, S.Y., Zhou, J., Xu, B.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.241 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor

Wang, X.Y., Tian, S.Y., Zhou, J., Xu, B.L.

To be published.

Biological Assembly 1  

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

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: 80.89 kDa 
• Atom Count: 5,948 
• Modeled Residue Count: 700 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 2	A, B	353	Homo sapiens	Mutation(s): 4  Gene Names: PARP2, ADPRT2, ADPRTL2 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGN5 (Homo sapiens) Explore Q9UGN5  Go to UniProtKB:  Q9UGN5
PHAROS:  Q9UGN5 GTEx:  ENSG00000129484

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D9M (Subject of Investigation/LOI)	D [auth A], E [auth B]	5-ethyl-1-[[3-[(3~{R})-4-ethyl-3-(2-hydroxyethyl)piperazin-1-yl]carbonyl-4-fluoranyl-phenyl]methyl]pyrimidine-2,4-dione C22 H29 F N4 O4 LLSYINGLAVMEEM-KRWDZBQOSA-N
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.241 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.34	α = 90
b = 86.239	β = 90.255
c = 95.221	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Wang, X.Y., Tian, S.Y., Zhou, J., Xu, B.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82104009

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release