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 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted B0RClick on this verticalbar to view details

This is version 1.3 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
307Homo 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
GTEx:  ENSG00000157764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.288 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
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



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted B0RClick on this verticalbar to view details

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
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations