3TV4 | pdb_00003tv4

Human B-Raf Kinase Domain in Complex with an Bromopyridine Benzamide Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.307 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3TV4

Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 71.33 kDa 
  • Atom Count: 4,378 
  • Modeled Residue Count: 540 
  • Deposited Residue Count: 614 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TV4

Query on TV4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
N-(6-amino-5-bromopyridin-3-yl)-2,6-difluoro-3-[(propylsulfonyl)amino]benzamide
C15 H15 Br F2 N4 O3 S
OJZKGEWGLIEDBZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TV4 BindingDB:  3TV4 IC50: min: 110, max: 1200 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.307 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.966α = 90
b = 107.966β = 90
c = 153.142γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNXrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2012-02-22
    Changes: Database references
  • Version 1.2: 2014-09-24
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations