SMTL ID : 5j42.1 (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: 9 residues within 4Å: Chain A: T.126, R.127, R.162, W.193, I.203, A.205, C.207, L.209 Ligands: TLA.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.127, A:W.193, A:A.205 Hydrogen bonds: A:T.126, A:R.162 Water bridges: A:R.127, A:R.127, A:R.162, A:D.163, A:D.163, A:D.163 pi-Cation interactions: A:R.127, A:R.162

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

TLA.2: 4 residues within 4Å: Chain A: T.126, R.127, G.128 Ligands: 6FV.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.126, A:R.127, A:R.127, A:G.128 Water bridges: A:T.126 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.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.125 Water bridges: A:N.16, A:N.16, A:N.16, A:Y.74, A:R.102 Salt bridges: A:R.102, A:H.122

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: K.138, L.141, G.142, Q.145, G.171, P.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.138, A:Q.145, A:G.171 Water bridges: A:G.142

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

EDO.5: 4 residues within 4Å: Chain A: R.162, D.163, L.209, R.213 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.163, A:D.163, A:R.213 Water bridges: A:R.210, A:R.210, A:R.210, A:R.210

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

MN.6: 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.2, H2O.5

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
A

Tyrosyl-DNA phosphodiesterase 2

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