SMTL ID : 6nrh.1

Crystal Structure of human PARP-1 ART domain bound inhibitor UTT63

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x KYP: 3-hydroxy-2-({4-[4-(pyrimidin-2-yl)piperazine-1-carbonyl]phenyl}methyl)-1-benzofuran-7-carboxamide(Non-covalent)

KYP.1: 13 residues within 4Å: Chain A: H.121, G.122, N.127, G.147, Y.148, Y.155, F.156, A.157, K.162, S.163, Y.166, E.247 Ligands: DMS.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.148, A:Y.148, A:Y.155, A:Y.155, A:Y.166, A:Y.166, A:Y.166 Hydrogen bonds: A:G.122, A:G.122 Water bridges: A:R.137, 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.244, A:Y.245, A:Y.245 Water bridges: A:K.162 Salt bridges: A:K.162 SO4.3: 4 residues within 4Å: Chain A: K.212, N.239, D.240, T.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.240, A:T.241, A:T.241 Salt bridges: A:K.212 SO4.4: 3 residues within 4Å: Chain A: E.99, N.257, K.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.99, A:N.257 Salt bridges: A:K.97, A:K.259 SO4.5: 3 residues within 4Å: Chain A: R.117, M.188, K.208 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.208, A:K.208 Salt bridges: A:R.117, A:K.208 SO4.6: 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

2 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: KYP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.155 DMS.8: 4 residues within 4Å: Chain A: K.57, T.58, D.59, E.101 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.59 Salt bridges: A:D.59

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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