8JNB

CRAF ras-binding domain chimera, ligand complex

• PDB DOI: https://doi.org/10.2210/pdb8JNB/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-06-06 Released: 2024-06-19 
• Deposition Author(s): Kawamura, T., Kumasaka, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.242 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers

Yoshikawa, Y., Makino, Y., Kubota, H., Kawamura, T., Matsumoto, S., Yuki, H., Shibaike, A., Okamura, M., Okada, T., Kataoka, T., Honma, T., Kumasaka, T., Koyama, H., Shima, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.89 kDa 
• Atom Count: 738 
• Modelled Residue Count: 81 
• Deposited Residue Count: 94 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAF proto-oncogene serine/threonine-protein kinase, CRaf	A [auth B]	94	Homo sapiens	Mutation(s): 4  Gene Names: RAF1, RAF, BRAF, BRAF1, RAFB1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04049 (Homo sapiens) Explore P04049  Go to UniProtKB:  P04049
PHAROS:  P04049 GTEx:  ENSG00000132155
Find proteins for P15056 (Homo sapiens) Explore P15056  Go to UniProtKB:  P15056
PHAROS:  P15056 GTEx:  ENSG00000157764
UniProt Groups	P15056P04049

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
USX (Subject of Investigation/LOI)	B	2-[4-[[(2S)-1-ethanoyl-3-oxidanylidene-2H-indol-2-yl]methyl]-2-methoxy-phenoxy]ethanamide C20 H20 N2 O5 DUXGCVPXJWCVOO-INIZCTEOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.242 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.019	α = 90
b = 69.775	β = 90
c = 39.746	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Kawamura, T., Kumasaka, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	17nk0101309h0003
Japan Science and Technology	Japan	22-20103170

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release