3TV6

Human B-Raf Kinase Domain in Complex with a Methoxypyrazolopyridinyl Benzamide Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pyrazolopyridine Inhibitors of B-Raf(V600E). Part 1: The Development of Selective, Orally Bioavailable, and Efficacious Inhibitors.

Wenglowsky, S.Ren, L.Ahrendt, K.A.Laird, E.R.Aliagas, I.Alicke, B.Buckmelter, A.J.Choo, E.F.Dinkel, V.Feng, B.Gloor, S.L.Gould, S.E.Gross, S.Gunzner-Toste, J.Hansen, J.D.Hatzivassiliou, G.Liu, B.Malesky, K.Mathieu, S.Newhouse, B.Raddatz, N.J.Ran, Y.Rana, S.Randolph, N.Risom, T.Rudolph, J.Savage, S.Selby, L.T.Shrag, M.Song, K.Sturgis, H.L.Voegtli, W.C.Wen, Z.Willis, B.S.Woessner, R.D.Wu, W.I.Young, W.B.Grina, J.

(2011) ACS Med Chem Lett 2: 342-347

  • DOI: 10.1021/ml200025q
  • Primary Citation of Related Structures:  
    3TV4, 3TV6

  • PubMed Abstract: 
  • The V600E mutation of B-Raf kinase results in constitutive activation of the MAPK signaling pathway and is present in approximately 7% of all cancers. Using structure-based design, a novel series of pyrazolopyridine inhibitors of B-Raf(V600E) was developed ...

    The V600E mutation of B-Raf kinase results in constitutive activation of the MAPK signaling pathway and is present in approximately 7% of all cancers. Using structure-based design, a novel series of pyrazolopyridine inhibitors of B-Raf(V600E) was developed. Optimization led to the identification of 3-methoxy pyrazolopyridines 17 and 19, potent, selective, and orally bioavailable agents that inhibited tumor growth in a mouse xenograft model driven by B-Raf(V600E) with no effect on body weight. On the basis of their in vivo efficacy and preliminary safety profiles, 17 and 19 were selected for further preclinical evaluation.


    Organizational Affiliation

    Array BioPharma, 3200 Walnut Street, Boulder, Colorado 80301, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-rafA, B307Homo sapiensMutation(s): 0 
Gene Names: BRAFBRAF1RAFB1
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
NIH Common Fund Data Resources
PHAROS:  P15056
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B0R
Query on B0R

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]2,6-difluoro-N-(3-methoxy-2H-pyrazolo[3,4-b]pyridin-5-yl)-3-[(propylsulfonyl)amino]benzamide
C17 H17 F2 N5 O4 S
PFHJLTOLXWXCJH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B0RIC50 :  4.800000190734863   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.44α = 90
b = 108.44β = 90
c = 150.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNXrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description