5ENN: Human VPS34

The crystal structure of Human VPS34 in complex with a selective and potent inhibitor. Determined by X-ray diffraction at 2.7 Å resolution. Released 16 Nov 2016.

Method

X-ray diffraction

Resolution

2.7 Å

Organism

Homo sapiens

Chains

2

Atoms

8,823

Mol. weight

144.71 kDa

Ligands

5QS

Released

16 Nov 2016

Explore 5ENN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ENN contains 64 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: 32 helices, 12 β-strands

Molecules and chains

>5ENN_1 Phosphatidylinositol 3-kinase catalytic subunit type 3 (chains A, B)
MSYYHHHHHHDYDIPTTENLYFQGAMGSGIRDQLNIIVSYPPTKQLTYEEQDLVWKFRYY
LTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVA
RLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDS
SQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECE
DQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRE
SGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLF
FKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFM
QFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVG
DRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQC
YTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSL
IDESVHALFAAVVEQIHKFAQYWRK

Ligands and cofactors

Water and common crystallization additives (SO4, GOL, NA) are not listed.

Primary citation

Potent, selective, and orally bioavailable inhibitors of VPS34 provide chemical tools to modulate autophagy in vivo. Kearney, E.P. To be published.

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
• 7RSP 1.67 Å, Structure of the VPS34 kinase domain with compound 14
• 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…

Browse structure collections

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