Crystals Structure of B-Raf kinase domain in complex with an Imidazopyridinyl benzamide inhibitor

Experimental Data Snapshot

  • Resolution: 2.68 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Imidazo[1,2-a]pyridin-6-yl-benzamide analogs as potent RAF inhibitors.

Smith, A.Ni, Z.J.Poon, D.Huang, Z.Chen, Z.Zhang, Q.Tandeske, L.Merritt, H.Shoemaker, K.Chan, J.Kaufman, S.Huh, K.Murray, J.Appleton, B.A.Cowan-Jacob, S.W.Scheufler, C.Kanazawa, T.Jansen, J.M.Stuart, D.Shafer, C.M.

(2017) Bioorg Med Chem Lett 27: 5221-5224

  • DOI: https://doi.org/10.1016/j.bmcl.2017.10.047
  • Primary Citation of Related Structures:  
    5MZ3, 6B8U

  • PubMed Abstract: 

    A series of imidazo[1,2-a]pyridin-6-yl-benzamide analogs was designed as inhibitors of B-RAF V600E . Medicinal chemistry techniques were employed to explore the SAR for this series and improve selectivity versus P38 and VEGFR2.

  • Organizational Affiliation

    Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, CA 94608, United States.

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 
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
GTEx:  ENSG00000157764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8EN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C24 H19 F3 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
8EN BindingDB:  6B8U IC50: 0.2 (nM) from 1 assay(s)
EC50: 230 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.68 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.502α = 90
b = 93.502β = 90
c = 164.703γ = 90
Software Package:
Software NamePurpose
PROCESSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description