6GJ7

CRYSTAL STRUCTURE OF KRAS G12D (GPPCP) IN COMPLEX WITH 22

• PDB DOI:  https://doi.org/10.2210/pdb6GJ7/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-05-16 Released: 2019-07-31 
• Deposition Author(s): Kessler, D., Mcconnell, D.M., Mantoulidis, A.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.257 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 

Literature

Drugging an undruggable pocket on KRAS.

Kessler, D., Gmachl, M., Mantoulidis, A., Martin, L.J., Zoephel, A., Mayer, M., Gollner, A., Covini, D., Fischer, S., Gerstberger, T., Gmaschitz, T., Goodwin, C., Greb, P., Haring, D., Hela, W., Hoffmann, J., Karolyi-Oezguer, J., Knesl, P., Kornigg, S., Koegl, M., Kousek, R., Lamarre, L., Moser, F., Munico-Martinez, S., Peinsipp, C., Phan, J., Rinnenthal, J., Sai, J., Salamon, C., Scherbantin, Y., Schipany, K., Schnitzer, R., Schrenk, A., Sharps, B., Siszler, G., Sun, Q., Waterson, A., Wolkerstorfer, B., Zeeb, M., Pearson, M., Fesik, S.W., McConnell, D.B.

(2019) Proc Natl Acad Sci U S A 116: 15823-15829

• PubMed: 31332011 
• DOI: https://doi.org/10.1073/pnas.1904529116
• Primary Citation of Related Structures:  
  6GJ5, 6GJ6, 6GJ7, 6GJ8


• PubMed Abstract: 
  

The 3 human RAS genes, KRAS, NRAS, and HRAS, encode 4 different RAS proteins which belong to the protein family of small GTPases that function as binary molecular switches involved in cell signaling. Activating mutations in RAS are among the most common oncogenic drivers in human cancers, with KRAS being the most frequently mutated oncogene. Although KRAS is an excellent drug discovery target for many cancers, and despite decades of research, no therapeutic agent directly targeting RAS has been clinically approved. Using structure-based drug design, we have discovered BI-2852 (1), a KRAS inhibitor that binds with nanomolar affinity to a pocket, thus far perceived to be "undruggable," between switch I and II on RAS; 1 is mechanistically distinct from covalent KRAS ^G12C inhibitors because it binds to a different pocket present in both the active and inactive forms of KRAS. In doing so, it blocks all GEF, GAP, and effector interactions with KRAS, leading to inhibition of downstream signaling and an antiproliferative effect in the low micromolar range in KRAS mutant cells. These findings clearly demonstrate that this so-called switch I/II pocket is indeed druggable and provide the scientific community with a chemical probe that simultaneously targets the active and inactive forms of KRAS.

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Organizational Affiliation: 

Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 20.44 kDa 
• Atom Count: 1,612 
• Modelled Residue Count: 166 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A	170	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCP	C [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C11 H18 N5 O13 P3 PHBDHXOBFUBCJD-KQYNXXCUSA-N
F0B	D [auth A]	(3~{S})-5-oxidanyl-3-[2-[[[1-(phenylmethyl)indol-6-yl]methylamino]methyl]-1~{H}-indol-3-yl]-2,3-dihydroisoindol-1-one C33 H28 N4 O2 ODHMZVFKZVCZOB-YTTGMZPUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.257 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.79	α = 90
b = 116.672	β = 90
c = 91.802	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
AutoPROC	data scaling
Aimless	data scaling
BUSTER	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Kessler, D., Mcconnell, D.M., Mantoulidis, A.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	854341

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2019-08-07
  Changes: Data collection, Database references
• Version 1.2: 2019-08-14
  Changes: Data collection, Database references