SMTL ID : 5j3z.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 6FQ: 2,4-dioxo-10-[3-(1H-tetrazol-5-yl)phenyl]-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile(Non-covalent)

6FQ.1: 8 residues within 4Å: Chain A: T.126, R.127, R.162, W.193, I.203, C.207, L.209 Ligands: GOL.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.127, A:W.193, A:I.203 Hydrogen bonds: A:R.127, A:R.127, A:R.162 Water bridges: A:G.128, A:G.128, A:D.163 pi-Cation interactions: A:R.162

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.18, E.48 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.18, A:E.48, H2O.1, H2O.2, H2O.9

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: W.193, D.244, H.245 Ligands: 6FQ.1, EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.245 Water bridges: A:E.48 GOL.4: 3 residues within 4Å: Chain A: G.142, Q.145, P.173 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.145

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

EDO.5: 4 residues within 4Å: Chain A: L.80, V.85, K.86, F.87 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.87 Water bridges: A:T.65, A:T.65, A:V.85 EDO.6: 7 residues within 4Å: Chain A: K.187, H.188, Q.190, Y.191, D.194, L.230, W.246 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.190, A:Y.191, A:Y.191, A:D.194 Water bridges: A:Q.190 EDO.7: 8 residues within 4Å: Chain A: N.70, E.71, E.72, Y.74, F.75, M.100, M.101, R.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.72 Water bridges: A:N.70, A:T.76, A:T.76 EDO.8: 4 residues within 4Å: Chain A: D.42, R.84 Ligands: EDO.10, EDO.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.42 Water bridges: A:S.40, A:S.40, A:R.84 EDO.9: 9 residues within 4Å: Chain A: N.16, E.48, H.122, S.125, D.158, N.160, F.211, H.245 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.125, A:D.158, A:N.160 Water bridges: A:R.102 EDO.10: 5 residues within 4Å: Chain A: T.9, D.42, L.111, G.112 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.9 EDO.11: 1 residues within 4Å: Ligands: EDO.8 No protein-ligand interaction detected (PLIP) EDO.12: 2 residues within 4Å: Chain A: I.134, K.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.168 Water bridges: A:K.168 EDO.13: 5 residues within 4Å: Chain A: R.127, S.130, D.163, E.165, K.168 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.127, A:S.130, A:E.165, A:K.168 Water bridges: A:K.168 EDO.14: 4 residues within 4Å: Chain A: H.188, S.227, L.228, D.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.228 Water bridges: A:H.188 EDO.15: 5 residues within 4Å: Chain A: N.175, F.177, R.217, A.218, E.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.218, A:E.220, A:E.220 Water bridges: A:E.220

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.16: 1 residues within 4Å: Chain A: L.38 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.38

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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