Human B-Raf Kinase in Complex with an Amide Linked Pyrazolopyridine Inhibitor

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

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Pyrazolopyridine inhibitors of B-RafV600E. Part 2: structure-activity relationships.

Wenglowsky, S.Ahrendt, K.A.Buckmelter, A.J.Feng, B.Gloor, S.L.Gradl, S.Grina, J.Hansen, J.D.Laird, E.R.Lunghofer, P.Mathieu, S.Moreno, D.Newhouse, B.Ren, L.Risom, T.Rudolph, J.Seo, J.Sturgis, H.L.Voegtli, W.C.Wen, Z.

(2011) Bioorg Med Chem Lett 21: 5533-5537

  • DOI: https://doi.org/10.1016/j.bmcl.2011.06.097
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Structure-activity relationships around a novel series of B-Raf(V600E) inhibitors are reported. The enzymatic and cellular potencies of inhibitors derived from two related hinge-binding groups were compared and3-methoxypyrazolopyridine proved to be superior. The 3-alkoxy group of lead B-Raf(V600E) inhibitor 1 was extended and minimally affected potency. The propyl sulfonamide tail of compound 1, which occupies the small lipophilic pocket formed by an outward shift of the αC-helix, was expanded to a series of arylsulfonamides. X-ray crystallography revealed that this lipophilic pocket unexpectedly enlarges to accommodate the bulkier aryl group.

  • Organizational Affiliation

    ArrayBioPharma, 3200 Walnut Street, Boulder, CO 80301, United States. wenglo1056@yahoo.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
307Homo 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 BR2

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H15 F2 N5 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
BR2 PDBBind:  3SKC IC50: 1.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.9α = 90
b = 107.9β = 90
c = 151.47γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata 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: 2011-08-17
    Type: Initial release
  • Version 1.1: 2011-12-14
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations