3EWH

Crystal structure of the VEGFR2 kinase domain in complex with a pyridyl-pyrimidine benzimidazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3EWH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2008-10-15 Released: 2009-08-25 
• Deposition Author(s): Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.206 

Literature

Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase.

Cee, V.J., Cheng, A.C., Romero, K., Bellon, S., Mohr, C., Whittington, D.A., Bak, A., Bready, J., Caenepeel, S., Coxon, A., Deak, H.L., Fretland, J., Gu, Y., Hodous, B.L., Huang, X., Kim, J.L., Lin, J., Long, A.M., Nguyen, H., Olivieri, P.R., Patel, V.F., Wang, L., Zhou, Y., Hughes, P., Geuns-Meyer, S.

(2009) Bioorg Med Chem Lett 19: 424-427

• PubMed: 19062275 
• DOI: https://doi.org/10.1016/j.bmcl.2008.11.056
• Primary Citation of Related Structures:  
  3DA6, 3EFW, 3EWH


• PubMed Abstract: 
  

  Selective small molecule inhibitors of Tie-2 kinase are important tools for the validation of Tie-2 signaling in pathological angiogenesis. Reported herein is the optimization of a nonselective scaffold into a potent and highly selective inhibitor of Tie-2 kinase.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Bldg. 1000, Cambridge, MA 02139, USA. [e-mail]

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: 36.71 kDa 
• Atom Count: 2,735 
• Modelled Residue Count: 300 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
vascular endothelial growth factor receptor 2	A	314	Homo sapiens	Mutation(s): 3  Gene Names: KDR, FLK1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens) Explore P35968  Go to UniProtKB:  P35968
PHAROS:  P35968 GTEx:  ENSG00000128052

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K11	B [auth A]	N-[4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)naphthalen-1-yl]-6-(trifluoromethyl)-1H-benzimidazol-2-amine C28 H20 F3 N7 O VIHXUAKPZPXVSW-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
K11	PDBBind:  3EWH	IC50: 69 (nM) from 1 assay(s)
	BindingDB:  3EWH	IC50: min: 69, max: 70 (nM) from 2 assay(s)
	Binding MOAD:  3EWH	IC50: 69 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.319	α = 90
b = 84.38	β = 99.33
c = 47.404	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
DENZO	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-23
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection