7RSP: VPS34 kinase domain with compound 14

Structure of the VPS34 kinase domain with compound 14. Determined by X-ray diffraction at 1.67 Å resolution. Released 24 Nov 2021.

Method

X-ray diffraction

Resolution

1.67 Å

Organism

Homo sapiens

Chains

2

Atoms

9,431

Mol. weight

140.98 kDa

Ligands

7IK

Released

24 Nov 2021

Explore 7RSP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RSP contains 65 α-helices and 24 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 33 helices, 12 β-strands

Molecules and chains

>7RSP_1 Phosphatidylinositol 3-kinase catalytic subunit type 3 (chains A, B)
HHHHHHGENLYFQGSDHDLKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQE
KALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQA
DDEDLLMYLLQLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIIT
SPLPSVSSPPPASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQ
QRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRK
KKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTED
GGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQS
VPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLD
NLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFL
HLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESV
HALFAAVVEQIH

Ligands and cofactors

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structure-Based Design of Potent, Selective, and Orally Bioavailable VPS34 Kinase Inhibitors. Hu, D.X., Patel, S., Chen, H. et al. J Med Chem (2022) 65:11500-11512. DOI 10.1021/acs.jmedchem.1c01180 · PubMed

Related structures

Other PDB entries of the same protein (UniProt Q8NEB9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 6HOG 1.26 Å, Structure of VPS34 LIR motif bound to GABARAP
• 7RSV 1.78 Å, Structure of the VPS34 kinase domain with compound 5
• 7RSJ 1.88 Å, Structure of the VPS34 kinase domain with compound 14
• 4UWH 1.93 Å, Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo-…
• 9NIN 2.01 Å, The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-86
• 8RXR 2.06 Å, Crystal structure of VPS34 in complex with inhibitor SB02024
• 9ORM 2.06 Å, The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-137
• 6I3U 2.09 Å, Optimization of potent and selective ATM inhibitors suitable for a proof-of-concept…
• 9ZF4 2.09 Å, The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-83
• 9DKP 2.16 Å, The structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53
• 3LS8 2.25 Å, Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimi…
• 6HOH 2.25 Å, Structure of VPS34 LIR motif (S249E) bound to GABARAP

Browse structure collections

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