SMTL ID : 8rxr.1 (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: 13 residues within 4Å: Chain A: F.333, P.339, I.355, K.357, Y.391, M.403, Q.404, F.405, I.406, S.408, L.471, I.481, D.482 8 PLIP interactions: 8 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, A:K.357, A:D.482

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: R.489, D.490, K.492, P.493 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.489 PEG.7: 3 residues within 4Å: Chain A: T.45, N.46, K.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.45

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 3 residues within 4Å: Chain A: T.389, P.390, Q.404 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.404, A:Q.404 Water bridges: A:K.477

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

DMS.4: 3 residues within 4Å: Chain A: L.114, Y.213, Y.217 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.370 DMS.5: 5 residues within 4Å: Chain A: W.60, H.91, Y.92, T.93, N.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.93, A:N.94 pi-Cation interactions: A:W.60 DMS.6: 4 residues within 4Å: Chain A: T.331, L.332, F.333, Q.341 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: T.96, R.99, E.193 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.99, A:R.106, A:E.193 Water bridges: A:R.99, A:A.103

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
A

Phosphatidylinositol 3-kinase catalytic subunit type 3

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