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


Ligand Structure Quality Assessment 


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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
307Homo sapiensMutation(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
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
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
Binding Affinity Annotations 
IDSourceBinding Affinity
B0R PDBBind:  3TV6 IC50: 4.8 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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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