SMTL ID : 8v0c.2 (1 other biounit)

Structure of TDP1 catalytic domain complexed with compound IB06

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

3 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: 8 residues within 4Å: Chain A: T.337, V.408, K.409, Q.410, V.425, Y.427, D.428, L.429 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.425, A:L.429, A:L.429 Water bridges: A:D.428 EDO.3: 6 residues within 4Å: Chain A: I.158, K.164, S.165, K.173, H.196 Ligands: PEG.5 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 YE3: (8M)-8-(2-{[2-(fluorosulfonyl)ethyl]amino}phenyl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid

YE3.4: 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.57, A:P.314, A:W.443 Hydrogen bonds: A:Y.57, A:N.136, A:N.136 Water bridges: A:Y.57, A:H.116, A:K.118, A:S.252, A:K.348 Salt bridges: A:H.116, A:K.118, A:H.346, A:K.348

1 x PEG: DI(HYDROXYETHYL)ETHER

PEG.5: 7 residues within 4Å: Chain A: S.165, K.173, A.174, I.177, S.178, H.196 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.165, A:S.178, A:S.178 Water bridges: A:E.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lountos, G.T. et al., Structures of TDP1 complexed with inhibitors. To Be Published

Release Date

2024-09-25

Peptides

Tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosyl-DNA phosphodiesterase 1

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