7Q9R | pdb_00007q9r

Cocrystal structure of PDE6D bound to NRAS peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.276 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.236 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Q9R

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.

Yelland, T.Garcia, E.Parry, C.Kowalczyk, D.Wojnowska, M.Gohlke, A.Zalar, M.Cameron, K.Goodwin, G.Yu, Q.Zhu, P.C.ElMaghloob, Y.Pugliese, A.Archibald, L.Jamieson, A.Chen, Y.X.McArthur, D.Bower, J.Ismail, S.

(2022) J Med Chem 65: 1898-1914

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01265
  • Primary Citation Related Structures: 
    7Q9Q, 7Q9R, 7Q9S, 7Q9U, 7QF9, 7QJK

  • PubMed Abstract: 

    RAS is a major anticancer drug target which requires membrane localization to activate downstream signal transduction. The direct inhibition of RAS has proven to be challenging. Here, we present a novel strategy for targeting RAS by stabilizing its interaction with the prenyl-binding protein PDE6D and disrupting its localization. Using rationally designed RAS point mutations, we were able to stabilize the RAS:PDE6D complex by increasing the affinity of RAS for PDE6D, which resulted in the redirection of RAS to the cytoplasm and the primary cilium and inhibition of oncogenic RAS/ERK signaling. We developed an SPR fragment screening and identified fragments that bind at the KRAS:PDE6D interface, as shown through cocrystal structures. Finally, we show that the stoichiometric ratios of KRAS:PDE6D vary in different cell lines, suggesting that the impact of this strategy might be cell-type-dependent. This study forms the foundation from which a potential anticancer small-molecule RAS:PDE6D complex stabilizer could be developed.


  • Organizational Affiliation
    • CRUK Beatson Institute, Glasgow G61 1BD, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 18.18 kDa 
  • Atom Count: 1,318 
  • Modeled Residue Count: 147 
  • Deposited Residue Count: 150 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit deltaA [auth BBB]150Homo sapiensMutation(s): 0 
Gene Names: PDE6DPDED
UniProt & NIH Common Fund Data Resources
Find proteins for O43924 (Homo sapiens)
Explore O43924 
Go to UniProtKB:  O43924
PHAROS:  O43924
GTEx:  ENSG00000156973 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43924
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAR
(Subject of Investigation/LOI)

Query on FAR



Download:Ideal Coordinates CCD File
B [auth BBB]FARNESYL
C15 H26
JXBSHSBNOVLGHF-BUJBXKITSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth BBB],
H [auth BBB],
I [auth BBB]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth BBB],
D [auth BBB],
E [auth BBB],
F [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.276 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.236 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.788α = 90
b = 55.788β = 90
c = 114.842γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description