SMTL ID : 7nr6.1

Structure of NUDT15 in complex with NSC56456

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: R.11, G.13, Y.90, H.91, Y.92 Chain B: F.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.91 EDO.4: 7 residues within 4Å: Chain A: F.52 Chain B: R.11, P.12, G.13, Y.90, H.91, Y.92 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.91

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.47, G.48, E.63, E.67 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.47, A:E.63, A:E.67, H2O.4, H2O.5 MG.5: 3 residues within 4Å: Chain B: G.47, E.63, E.67 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.47, B:E.63, B:E.67, H2O.8, H2O.11

2 x UO8: 2-azanyl-9-cyclohexyl-3~{H}-purine-6-thione(Non-covalent)

UO8.3: 13 residues within 4Å: Chain A: G.15, Q.44, L.45, P.46, G.47, G.48, H.49, Y.92, T.94, F.135, W.136, G.137, L.138 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.92, A:F.135, A:W.136 Hydrogen bonds: A:L.45, A:L.45, A:G.137 Water bridges: A:R.34, A:R.34, A:R.34 pi-Stacking: A:F.135, A:F.135 UO8.6: 14 residues within 4Å: Chain B: G.15, R.34, Q.44, L.45, P.46, G.47, G.48, H.49, Y.92, T.94, F.135, W.136, G.137, L.138 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.92, B:F.135, B:W.136 Hydrogen bonds: B:R.34, B:L.45, B:L.45, B:G.137 Water bridges: B:G.47 pi-Stacking: B:F.135, B:F.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valerie, N.C.K. et al., Coupling cellular target engagement to drug-induced responses with CeTEAM. To Be Published

Release Date

2022-03-23

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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