6ZL5

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

• PDB DOI: https://doi.org/10.2210/pdb6ZL5/pdb

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


• Deposited: 2020-06-30 Released: 2020-08-19 
• Deposition Author(s): Kessler, D., Fischer, G., Boettcher, J.

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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 

Starting Model: experimental

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

• PubMed: 32779487 
• DOI: https://doi.org/10.4155/fmc-2020-0221
• Primary Citation of Related Structures:  
  6ZIO, 6ZIR, 6ZIZ, 6ZJ0, 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. 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.

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Organizational Affiliation: 

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

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: 20.45 kDa 
• Atom Count: 1,574 
• Modelled Residue Count: 164 
• 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): 2  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 GTEx:  ENSG00000133703

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F0K (Subject of Investigation/LOI)	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
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
F0K	BindingDB:  6ZL5	Kd: 750 (nM) from 1 assay(s)
		IC50: 450 (nM) from 1 assay(s)

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 = 83.802	α = 90
b = 83.802	β = 90
c = 87.416	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Kessler, D., Fischer, G., Boettcher, J.

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2020-11-25
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description