9IM8: Poly [ADP-ribose] polymerase 2

Name: PDB 9IM8: Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor
Published: 2025-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor. Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Jul 2025.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,948
Mol. weight: 80.89 kDa
Ligands: A1D9M
Released: 9 Jul 2025

Explore 9IM8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IM8 contains 40 α-helices and 34 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	236-245	10
α-helix	248-257	10
β-strand	260	1	1
α-helix	267-269	3
α-helix	272-290	19
α-helix	296-308	13
β-strand	311	1	1
α-helix	317-320	4
α-helix	324-347	24
α-helix	357-363	7
β-strand	367-371	5	2
α-helix	377-388	12
β-strand	398-409	12	2
α-helix	412-415	4
β-strand	423-429	7	2
α-helix	432-434	3
α-helix	435-441	7
α-helix	445-447	3
α-helix	452-454	3
β-strand	461-463	3	3
β-strand	464	1	2
α-helix	467-471	5
α-helix	472-474	3
β-strand	482-491	10	2
β-strand	495-498	4	3
α-helix	505-508	4
β-strand	514-517	4	3
α-helix	518	1
β-strand	519-523	5	4
α-helix	525-527	3
β-strand	529-531	3	2
β-strand	534-536	3	2
β-strand	541-543	3	4
β-strand	554-556	3	4
β-strand	558-561	4	3
α-helix	564-566	3
β-strand	567-578	12	2

Chain B: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	236-245	10
α-helix	248-257	10
β-strand	260	1	5
α-helix	267-269	3
α-helix	272-290	19
α-helix	296-308	13
β-strand	311	1	5
α-helix	317-320	4
α-helix	324-347	24
α-helix	357-365	9
β-strand	367-371	5	6
α-helix	377-388	12
α-helix	392-394	3
β-strand	398-409	12	6
α-helix	412-415	4
β-strand	423-429	7	6
α-helix	432-434	3
α-helix	435-441	7
α-helix	445-447	3
α-helix	452-454	3
β-strand	461-463	3	7
β-strand	464	1	6
α-helix	467-472	6
β-strand	482-491	10	6
β-strand	495-498	4	7
α-helix	505-508	4
β-strand	514-517	4	7
β-strand	519-523	5	8
α-helix	525-527	3
β-strand	529-531	3	6
β-strand	534-536	3	6
α-helix	540	1
β-strand	541-543	3	8
β-strand	554-556	3	8
β-strand	558-561	4	7
α-helix	564-566	3
β-strand	567-578	12	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly [ADP-ribose] polymerase 2	A, B	protein	353	Homo sapiens	Q9UGN5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9IM8_1 Poly [ADP-ribose] polymerase 2 (chains A, B)
GPESQLDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDC
IRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVK
SERQGLEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVE
KDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSS
KSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHF
VTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQ

Ligands and cofactors

ID	Name	Formula	Copies
A1D9M	5-ethyl-1-[[3-[(3~{R})-4-ethyl-3-(2-hydroxyethyl)piperazin-1-yl]carbonyl-4-fluo…	C22 H29 F N4 O4	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor. Wang, X.Y., Tian, S.Y., Zhou, J. et al. To be published.

Other PDB entries of the same protein (UniProt Q9UGN5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ZZX 1.65 Å, Structure of PARP2 catalytic domain bound to an isoindolinone inhibitor
5D5K 1.9 Å, Crystal Structure NLS from human PARP-2 complexed with Importin alpha delta IBB
3KJD 1.95 Å, Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor…
3KCZ 2.0 Å, Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor…
7R59 2.0 Å, PARP2 catalytic domain in complex with OUL245
4TVJ 2.1 Å, Human ARTD2 (PARP2) - catalytic domain in complex with olaparib
8HKO 2.1 Å, Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib
9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
4ZZY 2.2 Å, Structure of human PARP2 catalytic domain bound to an isoindolinone inhibitor
6F1K 2.2 Å, Structure of ARTD2/PARP2 WGR domain bound to double strand DNA without 5'phosphate
8HLJ 2.24 Å, Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Olaparib…
9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2

Browse structure collections

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