3PSD

Non-oxime pyrazole based inhibitors of B-Raf kinase

• PDB DOI: https://doi.org/10.2210/pdb3PSD/pdb

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


• Deposited: 2010-12-01 Released: 2011-05-18 
• Deposition Author(s): Morales, T., Vigers, G.P.A., Brandhuber, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.335 
• R-Value Work: 0.277 
• R-Value Observed: 0.280 

Starting Model: experimental

Literature

Non-oxime pyrazole based inhibitors of B-Raf kinase.

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

(2011) Bioorg Med Chem Lett 21: 3488-3492

• PubMed: 21536432 
• DOI: https://doi.org/10.1016/j.bmcl.2010.12.038
• Primary Citation of Related Structures:  
  3PSD


• PubMed Abstract: 
  

  The synthesis and biological evaluation of non-oxime pyrazole based B-Raf inhibitors is reported. Several oxime replacements have been prepared and have shown excellent enzyme activity. Further optimization of fused pyrazole 2a led to compound 38, a selective and potent B-Raf inhibitor.

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Organizational Affiliation: 

Array BioPharma, 3200 Walnut Street, Boulder, CO 80301, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.2 kDa 
• Atom Count: 4,258 
• Modelled Residue Count: 526 
• 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
SM7	C [auth A], D [auth B]	6-[1-(piperidin-4-yl)-3-(pyridin-4-yl)-1H-pyrazol-4-yl]indeno[1,2-c]pyrazole C23 H20 N6 INSHJFDTYUIUOG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SM7	PDBBind:  3PSD	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.335 
• R-Value Work: 0.277 
• R-Value Observed: 0.280 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.98	α = 90
b = 94.98	β = 90
c = 161.73	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Morales, T., Vigers, G.P.A., Brandhuber, B.J.

Revision History  

• Version 1.0: 2011-05-18
  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: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description