11YC: PDB entry 11YC

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-123. Determined by X-ray diffraction at 2.41 Å resolution. Released 25 Mar 2026.

Method

X-ray diffraction

Resolution

2.41 Å

Organism

Homo sapiens

Chains

1

Atoms

4,342

Mol. weight

68.77 kDa

Ligands

A1DAY

Released

25 Mar 2026

Explore 11YC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

11YC contains 35 α-helices and 12 β-strands across 1 chain. 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 B: 35 helices, 12 β-strands

Molecules and chains

>11YC_1 Phosphatidylinositol 3-kinase catalytic subunit type 3 (chains B)
MGHHHHHHHHHHAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCV
NWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLL
QLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPP
PASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMY
LNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALL
GDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKH
GDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTE
GSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKL
FHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLIL
NLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALF

Ligands and cofactors

Water and common crystallization additives (CL, PEG, EDO) are not listed.

Primary citation

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-123. Abiodun, W.O., Litchfield, C.M., Burtch, M. et al. 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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