SMTL ID : 7ufy.1 (1 other biounit)

Crystal structure of TDP1 complexed with compound XZ766

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

1 x N8I: [(4-{[(4S)-2,7-diphenylimidazo[1,2-a]pyridin-3-yl]amino}phenyl)methyl]phosphonic acid(Non-covalent)

N8I.1: 5 residues within 4Å: Chain A: G.26, V.27, K.28, P.29, K.30 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.28, A:K.28, A:P.29 Hydrogen bonds: A:K.28, A:K.28, A:K.30 Water bridges: A:K.28 pi-Cation interactions: A:K.28

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

EDO.2: 9 residues within 4Å: Chain A: I.208, G.209, S.210, G.224, T.366, A.368, W.375, 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: 5 residues within 4Å: Chain A: I.158, K.164, S.165, K.173, H.196 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.173 Water bridges: A:K.164, A:K.164, A:S.165, A:H.196 EDO.4: 4 residues within 4Å: Chain A: S.51, E.190, W.191, V.194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.51, A:S.51 Water bridges: A:S.187, A:E.190, A:W.191 EDO.5: 8 residues within 4Å: Chain A: T.337, V.408, K.409, Q.410, V.425, Y.427, D.428, L.429 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.425, A:L.429, A:L.429

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, X.Z. et al., Phosphonic acid-containing inhibitors of tyrosyl-DNA phosphodiesterase 1. Front Chem (2022)

Release Date

2023-04-12

Peptides

Tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosyl-DNA phosphodiesterase 1

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