4AW5 | pdb_00004aw5

Complex of the EphB4 kinase domain with an oxindole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4AW5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-05-31 Released: 2012-08-01 
• Deposition Author(s): Till, J.H., Stout, T.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: other

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

• PubMed: 22765894 
• DOI: https://doi.org/10.1016/j.bmcl.2012.06.029
• Primary Citation 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. 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.39 kDa 
• Atom Count: 2,191 
• Modeled Residue Count: 261 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-B RECEPTOR 4	A	291	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000196411

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
30K	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.657	α = 90
b = 53.978	β = 111.06
c = 63.242	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Till, J.H., Stout, T.J.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description