6CCX

NMR data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a nanodisc


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 3000 
  • Conformers Submitted: 10 
  • Selection Criteria: 10 structures for lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site.

Fang, Z.Marshall, C.B.Nishikawa, T.Gossert, A.D.Jansen, J.M.Jahnke, W.Ikura, M.

(2018) Cell Chem Biol 25: 1327-1336.e4

  • DOI: 10.1016/j.chembiol.2018.07.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • KRAS is frequently mutated in several of the most lethal types of cancer; however, the KRAS protein has proven a challenging drug target. K-RAS4B must be localized to the plasma membrane by prenylation to activate oncogenic signaling, thus we endeavo ...

    KRAS is frequently mutated in several of the most lethal types of cancer; however, the KRAS protein has proven a challenging drug target. K-RAS4B must be localized to the plasma membrane by prenylation to activate oncogenic signaling, thus we endeavored to target the protein-membrane interface with small-molecule compounds. While all reported lead compounds have low affinity for KRAS in solution, the potency of Cmpd2 was strongly enhanced when prenylated K-RAS4B is associated with a lipid bilayer. We have elucidated a unique mechanism of action of Cmpd2, which simultaneously engages a shallow pocket on KRAS and associates with the lipid bilayer, thereby stabilizing KRAS in an orientation in which the membrane occludes its effector-binding site, reducing RAF binding and impairing activation of RAF. Furthermore, enrichment of Cmpd2 on the bilayer enhances potency by promoting interaction with KRAS. This insight reveals a novel approach to developing inhibitors of membrane-associated proteins.


    Organizational Affiliation

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Basel 4002, Switzerland; Institute for Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich 8093, Switzerland.,Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada.,Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA.,Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Basel 4002, Switzerland.,Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada. Electronic address: mikura@uhnresearch.ca.,Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada. Electronic address: cmarshal@uhnresearch.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apolipoprotein A-I
A, C
200Homo sapiensMutation(s): 0 
Gene Names: APOA1
Find proteins for P02647 (Homo sapiens)
Go to Gene View: APOA1
Go to UniProtKB:  P02647
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
B
187Homo sapiensMutation(s): 1 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EWS
Query on EWS

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Download CCD File 
B
(2R,4S)-4-[(5-bromo-1H-indole-3-carbonyl)amino]-2-[(4-chlorophenyl)methyl]piperidin-1-ium
C21 H22 Br Cl N3 O
GGXKHDYKPGTZBA-DLBZAZTESA-O
 Ligand Interaction
17F
Query on 17F

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Download CCD File 
A, B, C
O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
1,2-Dioleoyl-sn-glycero-3-phospho-L-serine
C42 H78 N O10 P
WTBFLCSPLLEDEM-JIDRGYQWSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

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Download CCD File 
B
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
PCW
Query on PCW

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Download CCD File 
A, B, C
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
(Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 3000 
  • Conformers Submitted: 10 
  • Selection Criteria: 10 structures for lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2019-03-27
    Type: Data collection, Database references