SMTL ID : 5j42.2 (1 other biounit)

Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 6FV: 10-(4-hydroxyphenyl)-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile(Non-covalent)

6FV.1: 11 residues within 4Å: Chain A: T.126, R.127, R.162, R.164, W.193, I.203, C.207, L.209, F.211 Ligands: TLA.2, TLA.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.127, A:W.193, A:I.203, A:F.211 Hydrogen bonds: A:T.126, A:R.127, A:R.162, A:R.164 Water bridges: A:R.164 pi-Cation interactions: A:R.127, A:R.162

4 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.2: 5 residues within 4Å: Chain A: T.126, R.127, G.128 Ligands: 6FV.1, TLA.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.127, A:R.127, A:G.128 Water bridges: A:T.126, A:R.127, A:R.127 Salt bridges: A:R.127, A:R.127 TLA.3: 7 residues within 4Å: Chain A: D.18, L.20, E.48, R.102, H.122, S.125 Ligands: MN.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.48, A:R.102, A:S.125 Water bridges: A:N.16, A:N.16, A:N.16, A:Y.74, A:Y.74, A:Y.74 Salt bridges: A:R.102, A:H.122 TLA.4: 6 residues within 4Å: Chain A: R.162, D.163, R.164, Q.190, Y.191, L.209 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.163, A:D.163, A:D.163, A:R.164, A:Q.190 Water bridges: A:R.164, A:R.164, A:R.210, A:R.213, A:R.213 TLA.5: 4 residues within 4Å: Chain A: R.127, A.205 Ligands: 6FV.1, TLA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.127 Salt bridges: A:R.127

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: F.95, P.96, N.97, T.98, E.132, R.135, T.139 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.97, A:N.97, A:T.98, A:E.132, A:R.135, A:R.135, A:T.139, A:T.139

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

EDO.7: 8 residues within 4Å: Chain A: K.187, H.188, C.189, Q.190, Y.191, D.194, L.230, W.246 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.187, A:Q.190, A:Y.191, A:D.194, A:D.194

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.8: 3 residues within 4Å: Chain A: D.18, E.48 Ligands: TLA.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.18, A:E.48, H2O.3, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hornyak, P. et al., Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2. Biochem.J. (2016)

Release Date

2016-05-04

Peptides

Tyrosyl-DNA phosphodiesterase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosyl-DNA phosphodiesterase 2

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