6ZL5

CRYSTAL STRUCTURE OF KRAS-G12D(C118S) IN COMPLEX WITH BI-2852 AND GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Drugging all RAS isoforms with one pocket.

Kessler, D.Bergner, A.Bottcher, J.Fischer, G.Dobel, S.Hinkel, M.Mullauer, B.Weiss-Puxbaum, A.McConnell, D.B.

(2020) Future Med Chem 12: 1911-1923

  • DOI: 10.4155/fmc-2020-0221
  • Primary Citation of Related Structures:  
    6ZIZ, 6ZIO, 6ZJ0, 6ZIR, 6ZL3, 6ZL5, 6ZLI

  • PubMed Abstract: 
  • Activating mutations in the three human RAS genes, KRAS , NRAS and HRAS , are among the most common oncogenic drivers in human cancers. Covalent KRAS G12C inhibitors, which bind to the switch II pocket in the 'off state' of KRAS, represent the first direct KRAS drugs that entered human clinical trials ...

    Activating mutations in the three human RAS genes, KRAS , NRAS and HRAS , are among the most common oncogenic drivers in human cancers. Covalent KRAS G12C inhibitors, which bind to the switch II pocket in the 'off state' of KRAS, represent the first direct KRAS drugs that entered human clinical trials. However, the remaining 85% of non-KRAS G12C -driven cancers remain undrugged as do NRAS and HRAS and no drugs targeting the 'on state' have been discovered so far. The switch I/II pocket is a second pocket for which the nanomolar inhibitor BI-2852 has been discovered. Here, we elucidate inhibitor binding modes in KRAS, NRAS and HRAS on and off and discuss future strategies to drug all RAS isoforms with this one pocket.


    Organizational Affiliation

    Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co. KG, 1121 Vienna, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasA170Homo sapiensMutation(s): 2 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
NIH Common Fund Data Resources
PHAROS:  P01116
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F0K
Query on F0K

Download Ideal Coordinates CCD File 
D [auth A](3~{S})-3-[2-[[[1-[(1-methylimidazol-4-yl)methyl]indol-6-yl]methylamino]methyl]-1~{H}-indol-3-yl]-5-oxidanyl-2,3-dihydroisoindol-1-one
C31 H28 N6 O2
JYEQLXOWWLNVDX-PMERELPUSA-N
 Ligand Interaction
GDP
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.802α = 90
b = 83.802β = 90
c = 87.416γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references