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

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 

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This is version 1.4 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Bldg. 1000, Cambridge, MA 02139, USA. vcee@amgen.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
vascular endothelial growth factor receptor 2314Homo sapiensMutation(s): 3 
Gene Names: KDRFLK1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
PHAROS:  P35968
GTEx:  ENSG00000128052 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35968
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on K11

Download Ideal Coordinates CCD File 
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
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding 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

  • 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 = 41.319α = 90
b = 84.38β = 99.33
c = 47.404γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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