4R5Y

The complex structure of Braf V600E kinase domain with a novel Braf inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


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Literature

BGB-283, a Novel RAF Kinase and EGFR Inhibitor, Displays Potent Antitumor Activity in BRAF-Mutated Colorectal Cancers.

Tang, Z., Yuan, X., Du, R., Cheung, S.H., Zhang, G., Wei, J., Zhao, Y., Feng, Y., Peng, H., Zhang, Y., Du, Y., Hu, X., Gong, W., Liu, Y., Gao, Y., Liu, Y., Hao, R., Li, S., Wang, S., Ji, J., Zhang, L., Li, S., Sutton, D., Wei, M., Zhou, C., Wang, L., Luo, L.

(2015) Mol Cancer Ther 14: 2187-2197

  • DOI: 10.1158/1535-7163.MCT-15-0262
  • Primary Citation of Related Structures:  
    4R5Y

  • PubMed Abstract: 

    • Oncogenic BRAF, which drives cell transformation and proliferation, has been detected in approximately 50% of human malignant melanomas and 5% to 15% of colorectal cancers. Despite the remarkable clinical activities achieved by vemurafenib and dabrafenib in treating BRAF(V600E) metastatic melanoma, their clinical efficacy in BRAF(V600E) colorectal cancer is far less impressive ...

    Oncogenic BRAF, which drives cell transformation and proliferation, has been detected in approximately 50% of human malignant melanomas and 5% to 15% of colorectal cancers. Despite the remarkable clinical activities achieved by vemurafenib and dabrafenib in treating BRAF(V600E) metastatic melanoma, their clinical efficacy in BRAF(V600E) colorectal cancer is far less impressive. Prior studies suggested that feedback activation of EGFR and MAPK signaling upon BRAF inhibition might contribute to the relative unresponsiveness of colorectal cancer to the first-generation BRAF inhibitors. Here, we report characterization of a dual RAF kinase/EGFR inhibitor, BGB-283, which is currently under clinical investigation. In vitro, BGB-283 potently inhibits BRAF(V600E)-activated ERK phosphorylation and cell proliferation. It demonstrates selective cytotoxicity and preferentially inhibits proliferation of cancer cells harboring BRAF(V600E) and EGFR mutation/amplification. In BRAF(V600E) colorectal cancer cell lines, BGB-283 effectively inhibits the reactivation of EGFR and EGFR-mediated cell proliferation. In vivo, BGB-283 treatment leads to dose-dependent tumor growth inhibition accompanied by partial and complete tumor regressions in both cell line-derived and primary human colorectal tumor xenografts bearing BRAF(V600E) mutation. These findings support BGB-283 as a potent antitumor drug candidate with clinical potential for treating colorectal cancer harboring BRAF(V600E) mutation.

    Organizational Affiliation: 

    Department of Discovery Biology, BeiGene (Beijing) Co., Ltd., Beijing, P.R. China. lusong.luo@beigene.com.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-rafA, B292Homo sapiensMutation(s): 17 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3K3
Query on 3K3
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		5-({(1R,1aS,6bR)-1-[5-(trifluoromethyl)-1H-benzimidazol-2-yl]-1a,6b-dihydro-1H-cyclopropa[b][1]benzofuran-5-yl}oxy)-3,4-dihydro-1,8-naphthyridin-2(1H)-one
C25 H17 F3 N4 O3
NGFFVZQXSRKHBM-FKBYEOEOSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3K3 BindingDB:  4R5Y IC50: 23 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.395α = 90
b = 101.601β = 90
c = 109.786γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description