SMTL ID : 4zzz.1

Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: K.251, L.332, L.333, Y.334 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.333, A:Y.334 Water bridges: A:S.331 Salt bridges: A:K.251 SO4.2: 3 residues within 4Å: Chain A: R.206, M.277, K.297 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.206, A:K.297 SO4.6: 5 residues within 4Å: Chain B: K.251, L.332, L.333, Y.334 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.333, B:Y.334, B:E.336 Salt bridges: B:K.251 SO4.8: 3 residues within 4Å: Chain B: R.206, M.277, K.297 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.206, B:K.297

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: D.114, R.226, I.227, A.228, Y.237, K.241, G.242, Y.244 Ligands: FSU.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.114, A:A.228, A:G.242 GOL.4: 8 residues within 4Å: Chain A: M.238, Y.244, K.251, Y.255, L.332, E.336 Ligands: SO4.1, FSU.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.251, A:Y.255, A:Y.255 GOL.7: 8 residues within 4Å: Chain B: M.238, Y.244, K.251, Y.255, L.332, E.336 Ligands: SO4.6, FSU.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.251, B:E.336 Water bridges: A:S.69

2 x FSU: 2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide(Non-covalent)

FSU.5: 12 residues within 4Å: Chain A: D.114, W.209, H.210, G.211, Y.244, F.245, A.246, S.252, Y.255, E.336 Ligands: GOL.3, GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.244, A:A.246, A:Y.255 Hydrogen bonds: A:G.211, A:G.211 pi-Stacking: A:Y.255 FSU.9: 10 residues within 4Å: Chain B: H.210, G.211, Y.244, F.245, A.246, K.251, S.252, Y.255, E.336 Ligands: GOL.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.244, B:A.246, B:Y.255, B:E.336 Hydrogen bonds: B:G.211, B:G.211 pi-Stacking: B:Y.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Papeo, G.M.E. et al., Discovery of 2-[1-(4,4-Difluorocyclohexyl)Piperidin-4-Yl]-6-Fluoro-3-Oxo-2,3-Dihydro-1H-Isoindole-4-Carboxamide (Nms-P118): A Potent, Orally Available and Highly Selective Parp- 1 Inhibitor for Cancer Therapy. J.Med.Chem. (2015)

Release Date

2015-08-12

Peptides

POLY [ADP-RIBOSE] POLYMERASE 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POLY [ADP-RIBOSE] POLYMERASE 1

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