8RXR: VPS34

Crystal structure of VPS34 in complex with inhibitor SB02024. Determined by X-ray diffraction at 2.06 Å resolution. Released 20 Mar 2024.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,463
Mol. weight: 138.8 kDa
Ligands: A1H4E
Released: 20 Mar 2024

Explore 8RXR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RXR contains 66 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

Element	Residues	Length	Sheet
α-helix	290-300	11
α-helix	306-309	4
α-helix	310-318	9
α-helix	320-323	4
α-helix	327-329	3
α-helix	330-334	5
α-helix	342-354	13
α-helix	356-359	4
α-helix	360-363	4
α-helix	364-367	4
α-helix	374-384	11
α-helix	389-402	14
α-helix	403-405	3
α-helix	408-413	6
α-helix	475-484	10
α-helix	487-501	15
α-helix	504-509	6
α-helix	511-529	19
α-helix	533-561	29
α-helix	566-578	13
α-helix	580-583	4
β-strand	591-593	3	1
β-strand	596-604	9	1
β-strand	610-611	2	1
β-strand	619-625	7	1
β-strand	630-637	8	1
α-helix	642-660	19
β-strand	672-674	3	1
β-strand	679-683	5	1
β-strand	688-689	2	2
α-helix	690-697	8
α-helix	700-707	8
β-strand	709	1	3
α-helix	714-716	3
β-strand	717	1	3
α-helix	719-739	21
β-strand	749-751	3	2
β-strand	757-759	3	2
α-helix	781-786	6
α-helix	793-811	19
α-helix	813-821	9
α-helix	829-832	4
α-helix	835-837	3
α-helix	838-846	9
α-helix	852-870	19

Chain B: 33 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	290-300	11
α-helix	306-309	4
α-helix	310-318	9
α-helix	320-323	4
α-helix	327-329	3
α-helix	330-334	5
α-helix	342-354	13
α-helix	356-359	4
α-helix	360-363	4
α-helix	364-367	4
α-helix	374-384	11
α-helix	389-402	14
α-helix	403-405	3
α-helix	408-413	6
α-helix	475-483	9
α-helix	487-501	15
α-helix	504-509	6
α-helix	511-529	19
α-helix	533-561	29
α-helix	566-578	13
β-strand	591-593	3	4
β-strand	596-604	9	4
α-helix	606-608	3
β-strand	610-611	2	4
β-strand	619-625	7	4
β-strand	630-637	8	4
α-helix	642-660	19
β-strand	672-674	3	4
β-strand	679-683	5	4
β-strand	688-689	2	5
α-helix	690-697	8
α-helix	700-707	8
β-strand	709	1	6
α-helix	714-716	3
β-strand	717	1	6
α-helix	719-739	21
β-strand	749-751	3	5
β-strand	757-759	3	5
α-helix	781-786	6
α-helix	793-811	19
α-helix	813-821	9
α-helix	829-832	4
α-helix	835-837	3
α-helix	838-845	8
α-helix	852-870	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 3-kinase catalytic subunit type 3	A, B	protein	600	Homo sapiens	Q8NEB9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8RXR_1 Phosphatidylinositol 3-kinase catalytic subunit type 3 (chains A, B)
SMSDHDLKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNW
DLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQL
VQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPA
SKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLN
VMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGD
NEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGD
DLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGS
IQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFH
IDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNL
FSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIH

Ligands and cofactors

ID	Name	Formula	Copies
A1H4E	4-[(3R)-3-methylmorpholin-4-yl]-2-[(2R)-2-(trifluoromethyl)piperidin-1-yl]-3H-p…	C16 H22 F3 N3 O2	2

Water and common crystallization additives (GOL, DMS, IMD, PEG) are not listed.

Primary citation

Combining VPS34 inhibitors with STING agonists enhances type I interferon signaling and anti-tumor efficacy. Yu, Y., Bogdan, M., Noman, M.Z. et al. Mol Oncol (2024) 18:1904-1922. DOI 10.1002/1878-0261.13619 · PubMed

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
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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