SMTL ID : 8otv.1

Crystal structure of NUDT14 complexed with novel compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x W0O: 1-(1-methylpiperidin-4-yl)-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-4-amine

W0O.1: 11 residues within 4Å: Chain A: S.34, W.35, D.36, G.148, L.149 Chain B: Y.18, S.43, R.63, A.106, L.108, Q.154 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Y.18, B:A.106, B:L.108, A:W.35, A:W.35, A:L.149 pi-Stacking: B:Y.18, B:Y.18, A:W.35, A:W.35, A:W.35 pi-Cation interactions: B:R.63 Hydrogen bonds: A:D.36, A:D.36 W0O.4: 8 residues within 4Å: Chain A: Y.18, R.63, L.108 Chain B: S.34, W.35, D.36, G.148, L.149 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Y.18, A:L.108, B:W.35, B:W.35, B:W.35, B:L.149 pi-Stacking: A:Y.18, A:Y.18, B:W.35, B:W.35, B:W.35 pi-Cation interactions: A:R.63 Hydrogen bonds: B:D.36, B:D.36

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 8 residues within 4Å: Chain A: A.141, T.142 Chain B: A.194, D.195, D.196, P.197, K.201, I.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.142

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: E.127, I.180 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.127, H2O.5, H2O.5, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balikci, E. et al., Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist. J.Med.Chem. (2024)

Release Date

2024-05-01

Peptides

Uridine diphosphate glucose pyrophosphatase NUDT14: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uridine diphosphate glucose pyrophosphatase NUDT14