SMTL ID : 7aop.1

Structure of NUDT15 in complex with inhibitor TH8321

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x RTW: 2-azanyl-9-cyclohexyl-8-(2-methoxyphenyl)-3~{H}-purine-6-thione(Non-covalent)

RTW.1: 16 residues within 4Å: Chain A: Q.44, L.45, P.46, G.47, G.48, H.49, E.67, S.83, I.85, Y.90, Y.92, T.94, F.135, W.136, G.137, L.138 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.85, A:Y.92, A:Y.92, A:W.136 Hydrogen bonds: A:L.45, A:G.47, A:G.137 Salt bridges: A:E.67 pi-Stacking: A:Y.92, A:F.135 RTW.3: 16 residues within 4Å: Chain B: Q.44, L.45, P.46, G.47, G.48, H.49, E.67, S.83, I.85, Y.90, Y.92, T.94, F.135, W.136, G.137, L.138 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.85, B:Y.92, B:Y.92, B:W.136 Hydrogen bonds: B:L.45, B:G.47, B:G.137 Salt bridges: B:E.67 pi-Stacking: B:Y.92, B:F.135

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: G.47, E.63, E.67 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.47, A:E.67, H2O.1, H2O.2, H2O.3 MG.4: 3 residues within 4Å: Chain B: G.47, E.63, E.67 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:G.47, B:E.67, H2O.3, H2O.4, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S.M. et al., NUDT15-mediated hydrolysis limits the efficacy of anti-HCMV drug ganciclovir. Cell Chem Biol (2021)

Release Date

2021-06-02

Peptides

Nucleotide triphosphate diphosphatase NUDT15: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nucleotide triphosphate diphosphatase NUDT15

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