5CT7

BRAF in Complex with RAF265

• PDB DOI: https://doi.org/10.2210/pdb5CT7/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-07-23 Released: 2015-09-09 
• Deposition Author(s): Appleton, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Discovery of RAF265: A Potent mut-B-RAF Inhibitor for the Treatment of Metastatic Melanoma.

Williams, T.E., Subramanian, S., Verhagen, J., McBride, C.M., Costales, A., Sung, L., Antonios-McCrea, W., McKenna, M., Louie, A.K., Ramurthy, S., Levine, B., Shafer, C.M., Machajewski, T., Renhowe, P.A., Appleton, B.A., Amiri, P., Chou, J., Stuart, D., Aardalen, K., Poon, D.

(2015) ACS Med Chem Lett 6: 961-965

• PubMed: 26396681 
• DOI: https://doi.org/10.1021/ml500526p
• Primary Citation of Related Structures:  
  5CT7


• PubMed Abstract: 
  

  Abrogation of errant signaling along the MAPK pathway through the inhibition of B-RAF kinase is a validated approach for the treatment of pathway-dependent cancers. We report the development of imidazo-benzimidazoles as potent B-RAF inhibitors. Robust in vivo efficacy coupled with correlating pharmacokinetic/pharmacodynamic (PKPD) and PD-efficacy relationships led to the identification of RAF265, 1, which has advanced into clinical trials.

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Organizational Affiliation: 

Global Discovery Chemistry, Oncology and Exploratory Chemistry, Novartis Institutes for Biomedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.86 kDa 
• Atom Count: 4,084 
• Modelled Residue Count: 511 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	281	Homo sapiens	Mutation(s): 0  Gene Names: BRAF, BRAF1, RAFB1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens) Explore P15056  Go to UniProtKB:  P15056
PHAROS:  P15056 GTEx:  ENSG00000157764

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
55J	C [auth A], D [auth B]	1-methyl-5-({2-[5-(trifluoromethyl)-1H-imidazol-2-yl]pyridin-4-yl}oxy)-N-[4-(trifluoromethyl)phenyl]-1H-benzimidazol-2-amine C24 H16 F6 N6 O YABJJWZLRMPFSI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
55J	BindingDB:  5CT7	Kd: min: 330, max: 1200 (nM) from 2 assay(s)
		IC50: min: 0.5, max: 140 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.38	α = 90
b = 109.38	β = 90
c = 158.13	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Appleton, B.A.

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-10-07
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations