SMTL ID : 7b67.1

Structure of NUDT15 V18_V19insGV Mutant in complex with TH7755

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x SYW: (R)-6-((2-methyl-4-(1-methyl-1H-indole-5-carbonyl)piperazin-1-yl)sulfonyl)benzo[d]oxazol-2(3H)-one(Non-covalent)

SYW.1: 19 residues within 4Å: Chain A: G.17, V.18, G.19, V.40, Q.46, L.47, P.48, G.50, H.51, E.90, N.91, Y.92, Y.94, T.96, F.137, W.138, G.139, L.140 Ligands: PO4.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.40, A:Y.94, A:T.96, A:W.138 Hydrogen bonds: A:V.18, A:L.47, A:L.47, A:G.139, A:L.140 Water bridges: A:R.36 pi-Stacking: A:Y.92, A:Y.92 SYW.4: 20 residues within 4Å: Chain B: G.17, V.18, G.19, R.36, V.40, F.45, Q.46, L.47, P.48, G.50, H.51, E.90, N.91, Y.92, Y.94, T.96, F.137, W.138, G.139, L.140 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.40, B:Y.94, B:T.96, B:W.138 Hydrogen bonds: B:V.18, B:L.47, B:L.47, B:G.139, B:L.140 Water bridges: B:R.36, B:R.36 pi-Stacking: B:Y.92, B:Y.92

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: G.50, H.51, E.53, E.65 Ligands: SYW.1, MG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.51 Water bridges: A:G.49, A:R.64, A:R.64, A:E.65, A:E.65, A:E.68, A:E.69, A:E.69 Salt bridges: A:H.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: G.49, E.65, E.69 Ligands: PO4.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.65, A:E.69, H2O.2, H2O.4, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rehling, D. et al., Crystal structures of NUDT15 variants enabled by a potent inhibitor reveal the structural basis for thiopurine sensitivity. J.Biol.Chem. (2021)

Release Date

2021-03-24

Peptides

Nucleotide triphosphate diphosphatase NUDT15: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nucleotide triphosphate diphosphatase NUDT15