4BB4

ephB4 kinase domain inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery and Optimization of a Novel Series of Potent Mutant B-Raf V600E Selective Kinase Inhibitors.

Vasbinder, M.M.Aquila, B.Augustin, M.Chen, H.Cheung, T.Cook, D.Drew, L.Fauber, B.P.Glossop, S.Grondine, M.Hennessy, E.J.Johannes, J.Lee, S.Lyne, P.D.Mortl, M.Omer, C.Palakurthi, S.Pontz, T.Read, J.Sha, L.Shen, M.Steinbacher, S.Wang, H.Wu, A.Ye, M.

(2013) J Med Chem 56: 1996

  • DOI: 10.1021/jm301658d
  • Primary Citation of Related Structures:  
    4BB4, 4H58

  • PubMed Abstract: 
  • B-Raf represents an attractive target for anticancer therapy and the development of small molecule B-Raf inhibitors has delivered new therapies for metastatic melanoma patients. We have discovered a novel class of small molecules that inhibit mutant B-Raf(V600E) kinase activity both in vitro and in vivo ...

    B-Raf represents an attractive target for anticancer therapy and the development of small molecule B-Raf inhibitors has delivered new therapies for metastatic melanoma patients. We have discovered a novel class of small molecules that inhibit mutant B-Raf(V600E) kinase activity both in vitro and in vivo. Investigations into the structure-activity relationships of the series are presented along with efforts to improve upon the cellular potency, solubility, and pharmacokinetic profile. Compounds selectively inhibited B-Raf(V600E) in vitro and showed preferential antiproliferative activity in mutant B-Raf(V600E) cell lines and exhibited selectivity in a kinase panel against other kinases. Examples from this series inhibit growth of a B-Raf(V600E) A375 xenograft in vivo at a well-tolerated dose. In addition, aminoquinazolines described herein were shown to display pERK elevation in nonmutant B-Raf cell lines in vitro.


    Organizational Affiliation

    Oncology iMED, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States. melissa.vasbinder@astrazeneca.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EPHRIN TYPE-B RECEPTOR 4A302Homo sapiensMutation(s): 1 
Gene Names: EPHB4HTKMYK1TYRO11
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54760 (Homo sapiens)
Explore P54760 
Go to UniProtKB:  P54760
PHAROS:  P54760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
32W
Query on 32W

Download Ideal Coordinates CCD File 
B [auth A]N-(2-methoxyethyl)-4-[(6-pyridin-4-ylquinazolin-2-yl)amino]benzamide
C23 H21 N5 O2
NXVFABZXYFFUBF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
32W PDBBind:  4BB4 IC50: 190 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.421α = 90
b = 53.329β = 111.5
c = 61.209γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references, Derived calculations
  • Version 1.2: 2018-04-04
    Changes: Data collection
  • Version 1.3: 2019-04-24
    Changes: Data collection, Source and taxonomy