3SKC

Human B-Raf Kinase in Complex with an Amide Linked Pyrazolopyridine Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3SKC/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2011-06-22 Released: 2011-08-17 
• Deposition Author(s): Voegtli, W.C., Sturgis, H.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.271 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

Literature

Pyrazolopyridine inhibitors of B-RafV600E. Part 2: structure-activity relationships.

Wenglowsky, S., Ahrendt, K.A., Buckmelter, A.J., Feng, B., Gloor, S.L., Gradl, S., Grina, J., Hansen, J.D., Laird, E.R., Lunghofer, P., Mathieu, S., Moreno, D., Newhouse, B., Ren, L., Risom, T., Rudolph, J., Seo, J., Sturgis, H.L., Voegtli, W.C., Wen, Z.

(2011) Bioorg Med Chem Lett 21: 5533-5537

• PubMed: 21802293 
• DOI: https://doi.org/10.1016/j.bmcl.2011.06.097
• Primary Citation of Related Structures:  
  3SKC


• PubMed Abstract: 
  

  Structure-activity relationships around a novel series of B-Raf(V600E) inhibitors are reported. The enzymatic and cellular potencies of inhibitors derived from two related hinge-binding groups were compared and3-methoxypyrazolopyridine proved to be superior. The 3-alkoxy group of lead B-Raf(V600E) inhibitor 1 was extended and minimally affected potency. The propyl sulfonamide tail of compound 1, which occupies the small lipophilic pocket formed by an outward shift of the αC-helix, was expanded to a series of arylsulfonamides. X-ray crystallography revealed that this lipophilic pocket unexpectedly enlarges to accommodate the bulkier aryl group.

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Organizational Affiliation: 

ArrayBioPharma, 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: 71.35 kDa 
• Atom Count: 4,355 
• Modelled Residue Count: 536 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	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
BR2	C [auth A], D [auth B]	2,6-difluoro-N-[(5S)-3-methoxy-5H-pyrazolo[3,4-b]pyridin-5-yl]-3-[(phenylsulfonyl)amino]benzamide C20 H15 F2 N5 O4 S AJASXPMSFTXFNS-NSHDSACASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BR2	PDBBind:  3SKC	IC50: 1.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.271 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.9	α = 90
b = 107.9	β = 90
c = 151.47	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
CNX	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Voegtli, W.C., Sturgis, H.L.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2011-12-14
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations