Human B-Raf Kinase Domain bound to a Type II Pyrazolopyridine Inhibitor

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 

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Pyrazolopyridine inhibitors of B-Raf(V600E). Part 4: Rational design and kinase selectivity profile of cell potent type II inhibitors.

Wenglowsky, S.Moreno, D.Laird, E.R.Gloor, S.L.Ren, L.Risom, T.Rudolph, J.Sturgis, H.L.Voegtli, W.C.

(2012) Bioorg Med Chem Lett 22: 6237-6241

  • DOI: https://doi.org/10.1016/j.bmcl.2012.08.007
  • Primary Citation of Related Structures:  
    4G9C, 4G9R

  • PubMed Abstract: 

    Cell potent inhibitors of B-Raf(V600E) that bind to the kinase in the DFG-out conformation are reported. These compounds utilize the hinge-binding group and lipophilic linker from a previously disclosed series of B-Raf(V600E) inhibitors that bind to the kinase in an atypical DFG-in, αC-helix-out conformation. This new series demonstrates that DFG-out kinase inhibitors can be rationally designed from related inhibitors which utilize an unconventional binding mode. Kinase selectivity profiles are compared. The pattern of kinase selectivity was found to be determined by the feature of the inhibitor which extends into the back pocket of the kinase and leads to the kinase conformation, rather than by the hinge-binding group or other minor modifications.

  • Organizational Affiliation

    Array BioPharma, 3200 Walnut Street, Boulder, CO 80301, 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
307Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0WP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C25 H20 F2 N6 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
0WP PDBBind:  4G9C IC50: 2.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.05α = 90
b = 107.05β = 90
c = 161.85γ = 90
Software Package:
Software NamePurpose
Blu-Icedata 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: 2012-11-14
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations