SMTL ID : 6t5j.1

Structure of NUDT15 in complex with inhibitor TH1760

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x MKB: 6-[4-(1~{H}-indol-5-ylcarbonyl)piperazin-1-yl]sulfonyl-3~{H}-1,3-benzoxazol-2-one(Non-covalent)

MKB.1: 17 residues within 4Å: Chain A: G.15, V.16, G.17, R.34, F.43, Q.44, L.45, P.46, G.47, G.48, Y.90, Y.92, T.94, F.135, W.136, G.137, L.138 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.16, A:L.45, A:L.45, A:G.137, A:L.138 Water bridges: A:R.34, A:R.34, A:E.88, A:E.88 pi-Stacking: A:Y.90, A:Y.90 pi-Cation interactions: A:H.49 MKB.5: 16 residues within 4Å: Chain B: G.15, V.16, G.17, R.34, Q.44, L.45, P.46, G.47, G.48, Y.90, Y.92, T.94, F.135, W.136, G.137, L.138 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.136 Hydrogen bonds: B:V.16, B:L.45, B:L.45, B:G.137, B:L.138 Water bridges: B:R.34, B:R.34, B:E.88 pi-Stacking: B:Y.90, B:Y.90 pi-Cation interactions: B:H.49

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: G.47, E.63, E.67 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.63, A:E.67, H2O.1, H2O.2, H2O.3, H2O.3 MG.3: 1 residues within 4Å: Chain A: E.51 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: G.47, E.63, E.67 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.63, B:E.67, H2O.9, H2O.10, H2O.11, H2O.13 MG.7: 1 residues within 4Å: Chain B: E.51 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: R.34, G.36, S.37, V.38 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: R.34, G.36, S.37, V.38 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S.M. et al., Development of a chemical probe against NUDT15. Nat.Chem.Biol. (2020)

Release Date

2020-07-29

Peptides

Probable 8-oxo-dGTP diphosphatase NUDT15: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable 8-oxo-dGTP diphosphatase NUDT15

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