SMTL ID : 6xvw.1 (1 other biounit)

Catalytic domain of human PARP-1 in complex with the inhibitor MC2050

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

4 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 1 residues within 4Å: Chain A: H.274 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.274 NI.2: 1 residues within 4Å: Chain A: H.277 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.277, H2O.3, H2O.3, H2O.6 NI.3: 1 residues within 4Å: Chain A: H.249 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.249, H2O.5, H2O.6, H2O.6 NI.4: 3 residues within 4Å: Chain A: H.162, H.166, D.170 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.162, A:H.166, A:D.170, H2O.1, H2O.5

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

EDO.5: 2 residues within 4Å: Chain A: K.7, P.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.7 EDO.6: 5 residues within 4Å: Chain A: K.14, F.17, P.129, I.130, N.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.129 EDO.7: 4 residues within 4Å: Chain A: Y.77, P.81, H.82, F.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.77, A:H.82 EDO.8: 1 residues within 4Å: Chain A: H.195 No protein-ligand interaction detected (PLIP) EDO.9: 2 residues within 4Å: Chain A: L.5, Q.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.7 EDO.10: 4 residues within 4Å: Chain A: S.51, S.54, P.222, E.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.51, A:P.222

1 x O3H: 2-[2-(4-pyridin-2-ylpiperazin-1-yl)ethylsulfanyl]-3~{H}-quinazolin-4-one(Non-covalent)

O3H.11: 17 residues within 4Å: Chain A: D.106, N.107, L.109, D.110, W.201, H.202, G.203, N.208, R.218, I.219, A.220, Y.236, F.237, K.243, S.244, Y.247, E.328 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.218, A:Y.236, A:K.243, A:Y.247 Hydrogen bonds: A:G.203, A:G.203 pi-Stacking: A:Y.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tomassi, S. et al., From PARP1 to TNKS2 Inhibition: A Structure-Based Approach. Acs Med.Chem.Lett. (2020)

Release Date

2020-06-03

Peptides

Poly [ADP-ribose] polymerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Poly [ADP-ribose] polymerase 1

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