SMTL ID : 5j3z.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: 10 residues within 4Å: Chain A: T.126, R.127, R.162, R.164, W.193, I.203, A.205, C.207, L.209, F.211 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.127, A:W.193, A:I.203, A:A.205, A:F.211 Hydrogen bonds: A:R.127, A:R.127, A:R.162, A:R.164, A:R.164 Water bridges: A:G.128, A:G.128 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.7

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: N.97, R.135 Ligands: GOL.4 No protein-ligand interaction detected (PLIP) GOL.4: 8 residues within 4Å: Chain A: F.95, P.96, N.97, T.98, E.132, R.135, T.139 Ligands: GOL.3 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

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

EDO.5: 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:H.188, A:Q.190, A:Y.191, A:D.194, A:D.194 EDO.6: 6 residues within 4Å: Chain A: C.35, Y.39, V.231, G.232, L.233, E.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.232, A:L.233, A:E.234 Water bridges: A:Y.39 EDO.7: 3 residues within 4Å: Chain A: I.93, K.143, E.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.143, A:E.146 EDO.8: 6 residues within 4Å: Chain A: D.163, W.180, Q.190, Y.191, R.210, R.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.163, A:Q.190, A:Q.190, A:R.210 Water bridges: A:R.210

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

ACT.9: 3 residues within 4Å: Chain A: K.82, G.83, V.85 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.82 Hydrogen bonds: A:G.83 Water bridges: A:F.87 ACT.10: 4 residues within 4Å: Chain A: I.66, I.67, T.68, E.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.68 Water bridges: A:T.68, A:E.71 ACT.11: 1 residues within 4Å: Chain A: G.83 No protein-ligand interaction detected (PLIP) ACT.12: 4 residues within 4Å: Chain A: W.193, F.211, D.244, H.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.48 Water bridges: A:N.16 Salt bridges: A:H.245 ACT.13: 5 residues within 4Å: Chain A: P.26, A.29, P.52, Y.53, Y.56 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.29, A:Y.56

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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