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 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    4AW5

  • 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 both biochemical and cellular potencies ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EPHRIN TYPE-B RECEPTOR 4A291Homo sapiensMutation(s): 0 
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
30K
Query on 30K

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
30K Binding MOAD:  4AW5 IC50: 765 (nM) from 1 assay(s)
PDBBind:  4AW5 IC50: 765 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.657α = 90
b = 53.978β = 111.06
c = 63.242γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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