9G4B | pdb_00009g4b

Human KRas4A (GDP) in complex with compound 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 
    0.193 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9G4B

Ligand Structure Quality Assessment 


This is version 1.1 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 68: 9129-9161

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02929
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 20.81 kDa 
  • Atom Count: 1,584 
  • Modeled Residue Count: 169 
  • Deposited Residue Count: 172 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IIU

Query on A1IIU



Download:Ideal Coordinates CCD File
G [auth A](3Z)-7-chloro-10,21-dihydroxy-2,2-dioxo-18-(4-piperidyl)-2-lambda-6,5-dithia-3,12,18-triazatetracyclo[18.3.1.04,12.06,11]tetracosa-1(23),3,6,8,10,20(24),21-heptaen-19-one
C24 H27 Cl N4 O5 S2
QLMCFQDRJDVMFQ-PNHLSOANSA-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],
F [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: 1.14 Å
  • R-Value Free:  0.193 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.01α = 90
b = 40.14β = 90
c = 110.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
PDB_EXTRACTdata extraction
XDSdata reduction

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: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references