SMTL ID : 8uzz.1 (1 other biounit)

Structure of TDP1 catalytic domain complexed with compound IB03

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

6 x EDO: 1,2-ETHANEDIOL

EDO.1: 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.2: 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.3: 3 residues within 4Å: Chain A: D.175, N.222, 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, L.123, E.190, W.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.51, A:S.51 Water bridges: A:S.187, 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:T.337, A:Q.410 EDO.6: 3 residues within 4Å: Chain A: P.44, E.71, F.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.71

1 x YA5: (8M)-8-{2-[(fluorosulfonyl)oxy]phenyl}-4-oxo-1,4-dihydroquinoline-3-carboxylic acid

YA5.7: 10 residues within 4Å: Chain A: Y.57, C.58, H.116, K.118, N.136, G.311, S.312, P.314, H.346, W.443 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.57, A:P.314, A:P.314, A:W.443 Hydrogen bonds: A:Y.57, A:N.136 Water bridges: A:K.118, A:K.118, A:K.348 Salt bridges: A:H.116, A:K.118, A:H.346, A:K.348

1 x PEG: DI(HYDROXYETHYL)ETHER

PEG.8: 6 residues within 4Å: Chain A: P.169, T.170, T.203, N.204, S.399, A.400 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.203 Water bridges: A:Y.206, A:Y.206, A:H.235

1 x DMS: DIMETHYL SULFOXIDE

DMS.9: 5 residues within 4Å: Chain A: H.327, S.328, Y.434, G.435, D.438 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lountos, G.T. et al., Structureal analysis of TDP1 in complex with inhbitors. 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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