SMTL ID : 6w7k.2 (1 other biounit)

Structure of Tdp1 catalytic domain in complex with inhibitor XZ634p

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x TG7: 4-[(2-phenylimidazo[1,2-a]pyridin-3-yl)amino]benzene-1,2-dicarboxylic acid(Non-covalent)

TG7.1: 10 residues within 4Å: Chain A: Y.57, H.116, K.118, N.136, S.252, S.312, P.314, H.346, K.348, N.369 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.314 Hydrogen bonds: A:N.136, A:S.252, A:N.369 Water bridges: A:K.118, A:K.348 Salt bridges: A:H.116, A:K.118, A:K.118, A:H.346, A:H.346, A:K.348, A:K.348 pi-Stacking: A:Y.57, A:H.116

3 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 EDO.3: 8 residues within 4Å: Chain A: T.337, V.408, K.409, Q.410, V.425, Y.427, D.428, L.429 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.425, A:L.429, A:L.429 Water bridges: A:Q.410, A:D.428 EDO.4: 5 residues within 4Å: Chain A: I.158, K.164, S.165, K.173, H.196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.164, A:K.173, A:H.196 Water bridges: A:K.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, X.Z. et al., Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites. Chemical Science (2021)

Release Date

2021-03-24

Peptides

Tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosyl-DNA phosphodiesterase 1

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