6CCH

NMR data-driven model of GTPase KRas-GMPPNP tethered to a nanodisc (E3 state)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 3000 
  • Conformers Submitted: 7 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasB187Homo sapiensMutation(s): 1 
Gene Names: KRAS, KRAS2, RASK2
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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
17F
Query on 17F
Download Ideal Coordinates CCD File 
AC [auth A],
BC [auth A],
CC [auth A],
DC [auth A],
EC [auth A],
AC [auth A],
BC [auth A],
CC [auth A],
DC [auth A],
EC [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth A],
XB [auth A],
YB [auth A],
ZB [auth A]
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 A],
AB [auth A],
BA [auth A],
BB [auth A],
CA [auth A],
AA [auth A],
AB [auth A],
BA [auth A],
BB [auth A],
CA [auth A],
CB [auth A],
D [auth A],
DA [auth A],
DB [auth A],
E [auth A],
EA [auth A],
EB [auth A],
F [auth A],
FA [auth A],
FB [auth A],
G [auth A],
GA [auth A],
GB [auth A],
H [auth A],
HA [auth A],
HB [auth A],
I [auth A],
IA [auth A],
IB [auth A],
J [auth A],
JB [auth A],
K [auth A],
KB [auth A],
L [auth A],
LB [auth A],
M [auth A],
MB [auth A],
N [auth A],
NB [auth A],
O [auth A],
OB [auth A],
P [auth A],
PB [auth A],
Q [auth A],
QB [auth A],
R [auth A],
RA [auth A],
RB [auth A],
S [auth A],
SA [auth A],
SB [auth A],
T [auth A],
TA [auth A],
TB [auth A],
U [auth A],
UA [auth A],
UB [auth A],
V [auth A],
VA [auth A],
VB [auth A],
W [auth A],
WA [auth A],
WB [auth A],
X [auth A],
XA [auth A],
Y [auth A],
YA [auth A],
Z [auth A],
ZA [auth A]
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 
FC [auth B]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
GC [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 3000 
  • Conformers Submitted: 7 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-03-27
    Changes: Data collection, Database references