SMTL ID : 9b3b.1 (1 other biounit)

Structure of TDP1 complexed with compound IB09

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

1 x 01: (8M)-8-{4-(benzylcarbamoyl)-2-[(fluorosulfonyl)oxy]phenyl}-4-oxo-1,4-dihydroquinoline-3-carboxylic acid

01.1: 9 residues within 4Å: Chain A: Y.57, H.116, K.118, N.136, G.311, S.312, P.314, H.346, W.443 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.57, A:P.314, A:W.443, A:W.443 Hydrogen bonds: A:N.136, A:H.346 Water bridges: A:K.348 Salt bridges: A:H.116, A:K.118, A:H.346, A:K.348

5 x EDO: 1,2-ETHANEDIOL

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: D.175, S.178, N.222, W.223, R.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.175, A:N.222 Water bridges: A:R.227 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:E.190, 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 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:V.425 EDO.6: 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

1 x DMS: DIMETHYL SULFOXIDE

DMS.7: 5 residues within 4Å: Chain A: H.327, Y.434, G.435, D.438, P.440 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lountos, G.T. et al., Structure of TDP1 complexed with compound IB09. To Be Published

Release Date

2024-09-25

Peptides

Tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosyl-DNA phosphodiesterase 1

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