SMTL ID : 8rxr.2 (1 other biounit)

Crystal structure of VPS34 in complex with inhibitor SB02024

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x 01: 4-[(3R)-3-methylmorpholin-4-yl]-2-[(2R)-2-(trifluoromethyl)piperidin-1-yl]-3H-pyridin-6-one

01.1: 14 residues within 4Å: Chain A: F.333, S.335, P.339, I.355, K.357, Y.391, M.403, Q.404, F.405, I.406, S.408, L.471, I.481, D.482 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.403, A:I.481, A:I.481 Hydrogen bonds: A:I.406, A:D.482 Water bridges: A:K.357

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

DMS.2: 3 residues within 4Å: Chain A: K.290, A.336, M.338 No protein-ligand interaction detected (PLIP) DMS.3: 4 residues within 4Å: Chain A: Q.34, D.35, C.57, E.65 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.35, A:E.65 DMS.4: 4 residues within 4Å: Chain A: T.331, L.332, F.333, Q.341 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.331 DMS.5: 5 residues within 4Å: Chain A: W.60, H.91, Y.92, T.93, N.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.93, A:T.93, A:N.94 pi-Cation interactions: A:W.60 DMS.6: 3 residues within 4Å: Chain A: L.114, Y.217, Q.370 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Y. et al., Combining VPS34 inhibitors with STING agonists enhances type I interferon signaling and anti-tumor efficacy. Mol Oncol (2024)

Release Date

2024-03-20

Peptides

Phosphatidylinositol 3-kinase catalytic subunit type 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Phosphatidylinositol 3-kinase catalytic subunit type 3

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