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

Structure of TDP1 catalytic domain complexed with compound IB02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x Y9G: 8-{[2-(fluorosulfonyl)ethyl]amino}-4-oxo-1,4-dihydroquinoline-3-carboxylic acid

Y9G.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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.57, A:P.314, A:W.443 Hydrogen bonds: A:Y.57, A:Y.57, A:Y.57, A:N.136 Water bridges: A:H.116, A:K.118, A:K.348, A:K.348, A:K.348 Salt bridges: A:H.116, A:K.118, A:H.346, A:K.348

2 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: 6 residues within 4Å: Chain A: I.158, K.164, S.165, K.173, H.196 Ligands: PEG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.173, A:H.196 Water bridges: A:K.164, A:K.164, A:H.196

1 x PEG: DI(HYDROXYETHYL)ETHER

PEG.4: 6 residues within 4Å: Chain A: S.165, K.173, A.174, I.177, H.196 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.167

1 x DMS: DIMETHYL SULFOXIDE

DMS.5: 8 residues within 4Å: Chain A: T.337, V.408, K.409, Q.410, V.425, Y.427, D.428, L.429 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.428

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lountos, G.T. et al., Structure of TDP1 catalytic domain complexed with compound IB02. 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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