SMTL ID : 8fz1.1 (1 other biounit)

Crystal structure of human PARP1 ART domain bound to inhibitor UKTT22 (compound 14)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 10 residues within 4Å: Chain A: F.110, L.200, P.201, K.202, G.203, K.204, H.205, Y.251, D.252, Q.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.203, A:K.204, A:K.204

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 8 residues within 4Å: Chain A: T.84, H.85, K.162, N.165, L.243, L.244, Y.245, E.247 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.84, A:N.165, A:L.244, A:Y.245, A:E.247 Salt bridges: A:H.85, A:H.85, A:K.162, A:K.162 CIT.5: 7 residues within 4Å: Chain A: Y.88, A.164, N.165, H.168, T.169, F.266 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.168, A:T.169 Salt bridges: A:H.168

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 8 residues within 4Å: Chain A: F.150, S.195, I.197, S.198, K.199, L.200, V.207, Y.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.195 DMS.6: 6 residues within 4Å: Chain A: H.121, R.137, G.153, Y.155 Ligands: YVB.4, EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.155

1 x YVB: (2P)-2-{3-[(2-amino-4,5-dimethylphenyl)carbamoyl]phenyl}-1H-benzimidazole-4-carboxamide(Non-covalent)

YVB.4: 16 residues within 4Å: Chain A: H.121, G.122, S.123, R.124, N.127, G.147, Y.148, Y.155, F.156, A.157, K.162, S.163, Y.166, E.247 Ligands: DMS.6, EDO.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.124, A:Y.148, A:Y.148, A:Y.155, A:Y.166, A:Y.166 Hydrogen bonds: A:G.122, A:G.122 Water bridges: A:Y.166, A:E.247 pi-Stacking: A:Y.166

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: N.165, H.168 Ligands: CIT.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.168 EDO.8: 7 residues within 4Å: Chain A: H.121, S.123, N.127, I.131, R.137 Ligands: YVB.4, DMS.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.123, A:N.127, A:R.137, A:R.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Velagapudi, U.K. et al., Novel modifications of PARP inhibitor veliparib increase PARP1 binding to DNA breaks. Biochem.J. (2024)

Release Date

2024-02-07

Peptides

Poly [ADP-ribose] polymerase 1, processed C-terminus: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Poly [ADP-ribose] polymerase 1, processed C-terminus

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