SMTL ID : 8cw2.2 (1 other biounit)

Crystal structure of TDP1 complexed with compound XZ760

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

1 x OYR: 4-({(4R)-7-phenyl-2-[4-(2-{[4-(pyridin-2-yl)phenyl]methoxy}ethyl)phenyl]imidazo[1,2-a]pyridin-3-yl}amino)benzene-1,2-dicarboxylic acid(Non-covalent)

OYR.1: 13 residues within 4Å: Chain A: Y.57, F.112, T.114, H.116, K.118, N.136, S.252, G.311, P.314, H.346, K.348, N.369, W.443 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:P.314, A:P.314, A:W.443 Hydrogen bonds: A:Y.57, A:N.136, A:S.252, A:N.369 Water bridges: A:K.118, A:H.346, A:K.348, A:K.348 Salt bridges: A:H.116, A:K.118, A:H.346, A:H.346, A:K.348, A:K.348 pi-Stacking: A:Y.57, A:H.116

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

EDO.2: 10 residues within 4Å: Chain A: I.208, G.209, S.210, G.224, T.366, A.368, W.375, E.391, L.392, G.393 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.210, A:G.224, A:T.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, X.Z. et al., Identification of multidentate tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors that simultaneously access the DNA, protein and catalytic-binding sites by oxime diversification. Rsc Chem Biol (2023)

Release Date

2023-04-12

Peptides

Tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosyl-DNA phosphodiesterase 1

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