9ILN | pdb_00009iln

ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9ILN/pdb

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


• Deposited: 2024-07-01 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: 2.49 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to a 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: 80.26 kDa 
• Atom Count: 5,801 
• Modeled Residue Count: 704 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 1, processed C-terminus	A, B	354	Homo sapiens	Mutation(s): 1  Gene Names: PARP1, ADPRT, PPOL EC: 2.4.2 (UniProt), 2.4.2.30 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens) Explore P09874  Go to UniProtKB:  P09874
PHAROS:  P09874 GTEx:  ENSG00000143799

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D9M (Subject of Investigation/LOI)	C [auth A], D [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
SO4	E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.505	α = 90
b = 91.967	β = 90
c = 164.079	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	82173693

Revision History  

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