4G9R

B-Raf V600E Kinase Domain Bound to a Type II Dihydroquinazoline Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.226 

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): 1 
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
B1E
Query on B1E
Download SDF File 
Download CCD File 
A, B
3-(2-cyanopropan-2-yl)-N-{4-methyl-3-[(3-methyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]phenyl}benzamide
C27 H25 N5 O2
ZGBGPEDJXCYQPH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B1EIC50: 2640 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.226 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.820α = 90.00
b = 96.820β = 90.00
c = 168.718γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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