4AW5

Complex of the EphB4 kinase domain with an oxindole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Design, Synthesis, and Biological Evaluation of Potent Receptor Tyrosine Kinase Inhibitors.

Kim, M.H.Tsuhako, A.L.Co, E.W.Aftab, D.T.Bentzien, F.Chen, J.Cheng, W.Engst, S.Goon, L.Klein, R.R.Le, D.T.Mac, M.Parks, J.J.Qian, F.Rodriquez, M.Stout, T.J.Till, J.H.Won, K.A.Wu, X.Michael Yakes, F.Yu, P.Zhang, W.Zhao, Y.Lamb, P.Nuss, J.M.Xu, W.

(2012) Bioorg.Med.Chem.Lett. 22: 4979

  • DOI: 10.1016/j.bmcl.2012.06.029

  • PubMed Abstract: 
  • Variously substituted indolin-2-ones were synthesized and evaluated for activity against KDR, Flt-1, FGFR-1 and PDGFR. Extension at the 5-position of the oxindole ring with ethyl piperidine (compound 7i) proved to be the most beneficial for attaining ...

    Variously substituted indolin-2-ones were synthesized and evaluated for activity against KDR, Flt-1, FGFR-1 and PDGFR. Extension at the 5-position of the oxindole ring with ethyl piperidine (compound 7i) proved to be the most beneficial for attaining both biochemical and cellular potencies. Further optimization of 7i to balance biochemical and cellular potencies with favorable ADME/ PK properties led to the identification of 8h, a compound with a clean CYP profile, acceptable pharmacokinetic and toxicity profiles, and robust efficacy in multiple xenograft tumor models.


    Organizational Affiliation

    Exelixis, 210 E. Grand Avenue, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPHRIN TYPE-B RECEPTOR 4
A
291Homo sapiensGene Names: EPHB4 (HTK, MYK1, TYRO11)
EC: 2.7.10.1
Find proteins for P54760 (Homo sapiens)
Go to Gene View: EPHB4
Go to UniProtKB:  P54760
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
30K
Query on 30K

Download SDF File 
Download CCD File 
A
(3Z)-5-[(1-ethylpiperidin-4-yl)amino]-3-[(5-methoxy-1H-benzimidazol-2-yl)(phenyl)methylidene]-1,3-dihydro-2H-indol-2-one
C30 H31 N5 O2
LETIJBVXDGOQFG-DQSJHHFOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
30KIC50: 765 nM BINDINGMOAD
30KIC50: 765 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.657α = 90.00
b = 53.978β = 111.06
c = 63.242γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-01
    Type: Initial release