4G9C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2012.08.007
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
307Homo sapiensMutation(s): 0 
Gene Names: BRAF (BRAF1, RAFB1)
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Go to Gene View: BRAF
Go to UniProtKB:  P15056
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0WP
Query on 0WP

Download SDF File 
Download CCD File 
A, B
3-{[3-(2-cyanopropan-2-yl)benzoyl]amino}-2,6-difluoro-N-(3-methoxy-2H-pyrazolo[3,4-b]pyridin-5-yl)benzamide
C25 H20 F2 N6 O3
BCTNUFBSYWOHHJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0WPIC50: 2.3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.050α = 90.00
b = 107.050β = 90.00
c = 161.850γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
Blu-Icedata collection
SCALAdata scaling
CNXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release