5CT7

BRAF in Complex with RAF265


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 55JClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
281Homo sapiensMutation(s): 0 
Gene Names: BRAFBRAF1RAFB1
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
55J
Query on 55J

Download Ideal Coordinates CCD File 
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 
IDSourceBinding 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 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.38α = 90
b = 109.38β = 90
c = 158.13γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 55JClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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