9GGY | pdb_00009ggy

Human KRas4A (GDP) in complex with compound 29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 
    0.194 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDPClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Reversible Small Molecule Multivariant Ras Inhibitors Display Tunable Affinity for the Active and Inactive Forms of Ras.

Parry, C.W.Pellicano, F.Schuttelkopf, A.W.Beyer, K.S.Bower, J.Bryson, A.Cameron, K.Cerutti, N.M.Clark, J.P.Davidson, S.C.Davies, K.Drysdale, M.J.Engelman, J.Estevan-Barber, A.Gohlke, A.Gray, C.H.Guthy, D.A.Hong, M.Hopkins, A.Hutchinson, L.D.Konczal, J.Maira, M.McArthur, D.Mezna, M.McKinnon, H.Nepravishta, R.Ostermann, N.Pasquali, C.C.Pollock, K.Pugliese, A.Rooney, N.Schmiedeberg, N.Shaw, P.Velez-Vega, C.West, C.West, R.Zecri, F.Taylor, J.B.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02929
  • Primary Citation of Related Structures:  
    9G0Y, 9G4B, 9GGT, 9GGU, 9GGV, 9GGW, 9GGX, 9GGY, 9GGZ, 9GH0, 9GH1, 9GH2

  • PubMed Abstract: 

    Activating mutations of Ras are one of the most prevalent drivers of cancer and are often associated with poor clinical outcomes. Despite FDA approval for two irreversible inhibitors that target the inactive state of KRas G12C , significant unmet clinical need still exists, and the susceptibility of non-G12C mutants to inactive-state inhibition remains unclear. Here we report the discovery of a novel series of reversible inhibitors that bind in an enlarged version of the switch I-II pocket with nanomolar affinities. Dependent on chemotype these can either preferentially bind to the inactive or active state or bind both with similar affinity. The active-state binders inhibit the Raf interaction for wild-type Ras, and a broad range of oncogenic KRas mutants with nanomolar potency. A subseries of these molecules displays cellular inhibition of Ras-Raf binding, as well as decreased phosphorylation of the downstream protein ERK, demonstrating that potent multivariant Ras inhibitors can be accessed from this novel pocket.


  • Organizational Affiliation

    Cancer Research Horizons, CRUK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas172Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IK3
Query on A1IK3

Download Ideal Coordinates CCD File 
F [auth A]12-(1-aza-5-azanidaspiro[4.5]decan-8-yl)-18-[(1-chloro-3-hydroxy-1,2,3-benzothiadiazol-5-yl)-lambda4-sulfanylidene]-4-hydroxy-3,3-dioxo-3lambda6-thia-1,4,12,17-tetraza-2lambda6-thia-6,10,19-triaza-3
C34 H41 Cl N6 O5 S2
GIQNFHLGMPQSSJ-OOKIHFLNSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free:  0.194 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.012α = 90
b = 40.37β = 90
c = 111.153γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release