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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02647
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
17F
Query on 17F

Download Ideal Coordinates CCD File 
BC [auth C],
CC [auth C],
DC [auth C],
EC [auth C],
FC [auth C],
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
Query on PCW

Download Ideal Coordinates CCD File 
AA [auth B],
AC [auth C],
BA [auth B],
BB [auth C],
CA [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
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
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 

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