3SKC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


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

  • 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 s ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
307Homo sapiensMutation(s): 0 
Gene Names: BRAF (BRAF1, RAFB1)
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Go to Gene View: BRAF
Go to UniProtKB:  P15056
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR2
Query on BR2

Download SDF File 
Download CCD File 
A, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BR2IC50: 1.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.900α = 90.00
b = 107.900β = 90.00
c = 151.470γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNXrefinement
CNSrefinement
CrystalCleardata collection
MOSFLMdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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