3D4Q

Pyrazole-based inhibitors of B-Raf kinase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 

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This is version 1.2 of the entry. See complete history. 


Literature

Potent and selective pyrazole-based inhibitors of B-Raf kinase.

Hansen, J.D., Grina, J., Newhouse, B., Welch, M., Topalov, G., Littman, N., Callejo, M., Gloor, S., Martinson, M., Laird, E., Brandhuber, B.J., Vigers, G., Morales, T., Woessner, R., Randolph, N., Lyssikatos, J., Olivero, A.

(2008) Bioorg Med Chem Lett 18: 4692-4695

  • DOI: https://doi.org/10.1016/j.bmcl.2008.07.002
  • Primary Citation of Related Structures:  
    3D4Q

  • PubMed Abstract: 

    • Herein we describe a novel pyrazole-based class of ATP competitive B-Raf inhibitors. These inhibitors exhibit both excellent cellular potency and striking B-Raf selectivity. A subset of these inhibitors has demonstrated the ability to inhibit downstream ERK phosphorylation in LOX tumors from mouse xenograft studies ...

    Herein we describe a novel pyrazole-based class of ATP competitive B-Raf inhibitors. These inhibitors exhibit both excellent cellular potency and striking B-Raf selectivity. A subset of these inhibitors has demonstrated the ability to inhibit downstream ERK phosphorylation in LOX tumors from mouse xenograft studies.

    Organizational Affiliation: 

    Lead Optimization, Array BioPharma, 3200 Walnut Street, Boulder, CO 80301, USA. josh.hansen@arraybiopharma.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
B-Raf proto-oncogene serine/threonine-protein kinaseA, B307Homo sapiensMutation(s): 0 
Gene Names: BRAF, BRAF1, RAFB1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
PHAROS:  P15056
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SM5
Query on SM5
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		(1E)-5-(1-piperidin-4-yl-3-pyridin-4-yl-1H-pyrazol-4-yl)-2,3-dihydro-1H-inden-1-one oxime
C22 H23 N5 O
KWEFZSZCLBHIEQ-YYADALCUSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SM5 BindingDB:  3D4Q IC50: min: 0.03, max: 9 (nM) from 2 assay(s)
PDBBind:  3D4Q IC50: 0.03 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.343α = 90
b = 100.343β = 90
c = 162.536γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary