8RXR | pdb_00008rxr

Crystal structure of VPS34 in complex with inhibitor SB02024


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.225 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.190 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8RXR

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Combining VPS34 inhibitors with STING agonists enhances type I interferon signaling and anti-tumor efficacy.

Yu, Y.Bogdan, M.Noman, M.Z.Parpal, S.Bartolini, E.Van Moer, K.Kleinendorst, S.C.Bilgrav Saether, K.Tresaugues, L.Silvander, C.Lindstrom, J.Simeon, J.Timson, M.J.Al-Hashimi, H.Smith, B.D.Flynn, D.L.Alexeyenko, A.Viklund, J.Andersson, M.Martinsson, J.Pokrovskaja Tamm, K.De Milito, A.Janji, B.

(2024) Mol Oncol 18: 1904-1922

  • DOI: https://doi.org/10.1002/1878-0261.13619
  • Primary Citation Related Structures: 
    8RXR

  • PubMed Abstract: 

    An immunosuppressive tumor microenvironment promotes tumor growth and is one of the main factors limiting the response to cancer immunotherapy. We have previously reported that inhibition of vacuolar protein sorting 34 (VPS34), a crucial lipid kinase in the autophagy/endosomal trafficking pathway, decreases tumor growth in several cancer models, increases infiltration of immune cells and sensitizes tumors to anti-programmed cell death protein 1/programmed cell death 1 ligand 1 therapy by upregulation of C-C motif chemokine 5 (CCL5) and C-X-C motif chemokine 10 (CXCL10) chemokines. The purpose of this study was to investigate the signaling mechanism leading to the VPS34-dependent chemokine increase. NanoString gene expression analysis was applied to tumors from mice treated with the VPS34 inhibitor SB02024 to identify key pathways involved in the anti-tumor response. We showed that VPS34 inhibitors increased the secretion of T-cell-recruitment chemokines in a cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes protein (STING)-dependent manner in cancer cells. Both pharmacological and small interfering RNA (siRNA)-mediated VPS34 inhibition increased cGAS/STING-mediated expression and secretion of CCL5 and CXCL10. The combination of VPS34 inhibitor and STING agonist further induced cytokine release in both human and murine cancer cells as well as monocytic or dendritic innate immune cells. Finally, the VPS34 inhibitor SB02024 sensitized B16-F10 tumor-bearing mice to STING agonist treatment and significantly improved mice survival. These results show that VPS34 inhibition augments the cGAS/STING pathway, leading to greater tumor control through immune-mediated mechanisms. We propose that pharmacological VPS34 inhibition may synergize with emerging therapies targeting the cGAS/STING pathway.


  • Organizational Affiliation
    • Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 138.8 kDa 
  • Atom Count: 9,463 
  • Modeled Residue Count: 1,076 
  • Deposited Residue Count: 1,200 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3
A, B
600Homo sapiensMutation(s): 0 
Gene Names: PIK3C3VPS34
EC: 2.7.1.137
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEB9 (Homo sapiens)
Explore Q8NEB9 
Go to UniProtKB:  Q8NEB9
PHAROS:  Q8NEB9
GTEx:  ENSG00000078142 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEB9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H4E
(Subject of Investigation/LOI)

Query on A1H4E



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
4-[(3R)-3-methylmorpholin-4-yl]-2-[(2R)-2-(trifluoromethyl)piperidin-1-yl]-3H-pyridin-6-one
C16 H22 F3 N3 O2
OTYQZXVFPRVZKW-DGCLKSJQSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth A],
I [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
L [auth B]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
E [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.225 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 288.824α = 90
b = 98.65β = 92.266
c = 62.895γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references
  • Version 1.2: 2024-08-21
    Changes: Database references