3IDP

B-Raf V600E kinase domain in complex with an aminoisoquinoline inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selective inhibitors of the mutant B-raf pathway: discovery of a potent and orally bioavailable aminoisoquinoline.

Smith, A.L.Demorin, F.F.Paras, N.A.Huang, Q.Petkus, J.K.Doherty, E.M.Nixey, T.Kim, J.L.Whittington, D.A.Epstein, L.F.Lee, M.R.Rose, M.J.Babij, C.Fernando, M.Hess, K.Le, Q.Beltran, P.Carnahan, J.

(2009) J.Med.Chem. 52: 6189-6192

  • DOI: 10.1021/jm901081g

  • PubMed Abstract: 
  • The discovery and optimization of a novel series of aminoisoquinolines as potent, selective, and efficacious inhibitors of the mutant B-Raf pathway is presented. The N-linked pyridylpyrimidine benzamide 2 was identified as a potent, modestly selectiv ...

    The discovery and optimization of a novel series of aminoisoquinolines as potent, selective, and efficacious inhibitors of the mutant B-Raf pathway is presented. The N-linked pyridylpyrimidine benzamide 2 was identified as a potent, modestly selective inhibitor of the B-Raf enzyme. Replacement of the benzamide with an aminoisoquinoline core significantly improved kinase selectivity and imparted favorable pharmacokinetic properties, leading to the identification of 1 as a potent antitumor agent in xenograft models.


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799, USA. adrians@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B-Raf proto-oncogene serine/threonine-protein kinase
B, A
300Homo sapiensMutation(s): 1 
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
L1E
Query on L1E

Download SDF File 
Download CCD File 
A, B
N~1~-(4-chlorophenyl)-6-methyl-N~5~-[3-(7H-purin-6-yl)pyridin-2-yl]isoquinoline-1,5-diamine
N5-(3-(9H-purin-6-yl)pyridin-2-yl)-N1-(4-chlorophenyl)-6-methylisoquinoline-1,5-diamine
C26 H19 Cl N8
KKVYYGGCHJGEFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L1EEC50: 1.8 nM (99) BINDINGDB
L1EKi: 1 nM (99) BINDINGDB
L1EIC50: 1.6 - 2 nM (99) BINDINGDB
L1EIC50: 1.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.457α = 90.00
b = 93.457β = 90.00
c = 166.679γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance