SMTL ID : 6nrg.1

Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT57

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x KYY: 2-{[3-fluoro-4-(1H-tetrazol-5-yl)phenyl]methyl}-3-hydroxy-1-benzofuran-7-carboxamide(Non-covalent)

KYY.1: 13 residues within 4Å: Chain A: H.121, G.122, T.146, G.147, Y.148, Y.155, F.156, A.157, K.162, S.163, Y.166, E.247 Ligands: DMS.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.148, A:Y.155, A:Y.166, A:Y.166 Hydrogen bonds: A:G.122, A:G.122 Water bridges: A:R.124, A:N.127, A:N.127, A:Y.166 pi-Stacking: A:Y.166

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

SO4.2: 4 residues within 4Å: Chain A: K.162, L.243, L.244, Y.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.244, A:Y.245, A:Y.245 Salt bridges: A:K.162 SO4.3: 3 residues within 4Å: Chain A: N.165, Y.166, H.168 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.165 Salt bridges: A:H.168 SO4.4: 4 residues within 4Å: Chain A: K.212, N.239, D.240, T.241 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.239, A:D.240, A:T.241 Water bridges: A:T.241 Salt bridges: A:K.212 SO4.5: 2 residues within 4Å: Chain A: N.257, K.259 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.257 Water bridges: A:E.99, A:K.111, A:K.111 Salt bridges: A:K.97, A:K.111, A:K.259 SO4.6: 5 residues within 4Å: Chain A: R.117, M.188, K.208 Ligands: DMS.8, DMS.9 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.208, A:K.208 Salt bridges: A:R.117, A:K.208

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

DMS.7: 7 residues within 4Å: Chain A: H.121, R.137, Y.148, G.153, I.154, Y.155 Ligands: KYY.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.155 DMS.8: 11 residues within 4Å: Chain A: R.117, D.158, K.208, T.214, P.215, N.220, P.229, N.246, Y.248 Ligands: SO4.6, DMS.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.220 Salt bridges: A:D.158 DMS.9: 6 residues within 4Å: Chain A: K.208, T.214, P.217, N.246 Ligands: SO4.6, DMS.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.208, A:N.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Velagapudi, U.K. et al., Design and Synthesis of Poly(ADP-ribose) Polymerase Inhibitors: Impact of Adenosine Pocket-Binding Motif Appendage to the 3-Oxo-2,3-dihydrobenzofuran-7-carboxamide on Potency and Selectivity. J.Med.Chem. (2019)

Release Date

2019-08-14

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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