6CC9

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:  
    6CC9, 6CCH, 6CCX

  • 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 endeavored to target the protein-membrane interface with small-molecule compounds ...

    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

    Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada. Electronic address: mikura@uhnresearch.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Apolipoprotein A-IA, C200Homo sapiensMutation(s): 0 
Gene Names: APOA1
UniProt & NIH Common Fund Data Resources
Find proteins for P02647 (Homo sapiens)
Explore P02647 
Go to UniProtKB:  P02647
PHAROS:  P02647
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasB187Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
17F (Subject of Investigation/LOI)
Query on 17F

Download Ideal Coordinates CCD File 
BC [auth C] , CC [auth C] , DC [auth C] , EC [auth C] , FC [auth C] , GC [auth C] , HC [auth C] , J [auth A] , 
BC [auth C],  CC [auth C],  DC [auth C],  EC [auth C],  FC [auth C],  GC [auth C],  HC [auth C],  J [auth A],  NA [auth B],  OA [auth B],  PA [auth B],  QA [auth B],  RA [auth B],  SA [auth B],  TA [auth B],  XA [auth B]
O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
C42 H78 N O10 P
WTBFLCSPLLEDEM-JIDRGYQWSA-N
 Ligand Interaction
PCW (Subject of Investigation/LOI)
Query on PCW

Download Ideal Coordinates CCD File 
AA [auth B] , AC [auth C] , BA [auth B] , BB [auth C] , CA [auth B] , CB [auth C] , D [auth A] , DA [auth B] , 
AA [auth B],  AC [auth C],  BA [auth B],  BB [auth C],  CA [auth B],  CB [auth C],  D [auth A],  DA [auth B],  DB [auth C],  E [auth A],  EA [auth B],  EB [auth C],  F [auth A],  FA [auth B],  FB [auth C],  G [auth A],  GA [auth B],  GB [auth C],  H [auth A],  HA [auth B],  HB [auth C],  I [auth A],  IA [auth B],  IB [auth C],  JA [auth B],  JB [auth C],  K [auth A],  KA [auth B],  KB [auth C],  L [auth A],  LA [auth B],  LB [auth C],  M [auth A],  MA [auth B],  MB [auth C],  N [auth A],  NB [auth C],  O [auth B],  OB [auth C],  P [auth B],  PB [auth C],  Q [auth B],  QB [auth C],  R [auth B],  RB [auth C],  S [auth B],  SB [auth C],  T [auth B],  TB [auth C],  U [auth B],  UA [auth B],  UB [auth C],  V [auth B],  VA [auth B],  VB [auth C],  W [auth B],  WA [auth B],  WB [auth C],  X [auth B],  XB [auth C],  Y [auth B],  YB [auth C],  Z [auth B],  ZB [auth C]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
YA [auth B]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
EWS (Subject of Investigation/LOI)
Query on EWS

Download Ideal Coordinates CCD File 
AB [auth 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
MG
Query on MG

Download Ideal Coordinates CCD File 
ZA [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 3000 
  • Conformers Submitted: 10 
  • Selection Criteria: 10 structures for lowest energy 
  • OLDERADO: 6CC9 Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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