3D4Q

Pyrazole-based inhibitors of B-Raf kinase

• PDB DOI: https://doi.org/10.2210/pdb3D4Q/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-05-14 Released: 2008-08-19 
• Deposition Author(s): Morales, T., Vigers, G.P.A., Brandhuber, B.J.

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Experimental Data Snapshot

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

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

• PubMed: 18676143 
• 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.

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Organizational Affiliation: 

Lead Optimization, Array BioPharma, 3200 Walnut Street, Boulder, CO 80301, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.18 kDa 
• Atom Count: 4,293 
• Modelled Residue Count: 528 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-Raf proto-oncogene serine/threonine-protein kinase	A, B	307	Homo sapiens	Mutation(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 GTEx:  ENSG00000157764

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SM5	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

Binding Affinity Annotations
ID	Source	Binding 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 = 100.343	α = 90
b = 100.343	β = 90
c = 162.536	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Morales, T., Vigers, G.P.A., Brandhuber, B.J.

Revision History  

• 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
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations