SMTL ID : 6nrj.1

Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT93

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x KYJ: (2Z)-2-[(4-{[2-(1H-benzimidazol-2-yl)ethyl]carbamoyl}phenyl)methylidene]-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide(Non-covalent)

KYJ.1: 19 residues within 4Å: Chain A: H.121, G.122, R.137, I.138, A.139, P.140, A.143, T.146, G.147, Y.148, Y.155, F.156, A.157, K.162, S.163, Y.166, E.247 Ligands: DMS.7, DMS.8 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.139, A:Y.148, A:Y.148, A:Y.155, A:A.157, A:Y.166, A:Y.166, A:E.247 Hydrogen bonds: A:G.122, A:G.122, A:Y.148 Water bridges: 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: 3 residues within 4Å: Chain A: N.165, Y.166, H.168 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.168 SO4.4: 4 residues within 4Å: Chain A: K.212, N.239, D.240, T.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.240, A:T.241 Salt bridges: A:K.212 SO4.5: 4 residues within 4Å: Chain A: K.97, E.99, N.257, K.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.99, A:N.257 Salt bridges: A:K.259 SO4.6: 3 residues within 4Å: Chain A: R.117, M.188, K.208 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.208, A:K.208, A:K.208, A:K.208, A:K.208 Salt bridges: A:R.117, A:K.208

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

DMS.7: 8 residues within 4Å: Chain A: H.121, R.137, Y.148, G.153, I.154, Y.155 Ligands: KYJ.1, DMS.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.155 DMS.8: 4 residues within 4Å: Chain A: N.127, R.137 Ligands: KYJ.1, DMS.7 No protein-ligand interaction detected (PLIP)

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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