3SKC

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    ArrayBioPharma, 3200 Walnut Street, Boulder, CO 80301, United States. wenglo1056@yahoo.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-rafA, B307Homo sapiensMutation(s): 0 
Gene Names: BRAFBRAF1RAFB1
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
BR2
Query on BR2

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 107.9α = 90
b = 107.9β = 90
c = 151.47γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2011-12-14
    Changes: Database references