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

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 

Starting Model: experimental
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Design, Synthesis, and Evaluation of Orally Active Benzimidazoles and Benzoxazoles as Vascular Endothelial Growth Factor-2 Receptor Tyrosine Kinase Inhibitors.

Potashman, M.H.Bready, J.Coxon, A.Demelfi, T.M.Dipietro, L.Doerr, N.Elbaum, D.Estrada, J.Gallant, P.Germain, J.Gu, Y.Harmange, J.C.Kaufman, S.A.Kendall, R.Kim, J.L.Kumar, G.N.Long, A.M.Neervannan, S.Patel, V.F.Polverino, A.Rose, P.Plas, S.V.Whittington, D.Zanon, R.Zhao, H.

(2007) J Med Chem 50: 4351-4373

  • DOI: https://doi.org/10.1021/jm070034i
  • Primary Citation of Related Structures:  
    2QU5, 2QU6

  • PubMed Abstract: 

    Inhibition of the VEGF signaling pathway has become a valuable approach in the treatment of cancers. Guided by X-ray crystallography and molecular modeling, a series of 2-aminobenzimidazoles and 2-aminobenzoxazoles were identified as potent inhibitors of VEGFR-2 (KDR) in both enzymatic and HUVEC cellular proliferation assays. In this report we describe the synthesis and structure-activity relationship of a series of 2-aminobenzimidazoles and benzoxazoles, culminating in the identification of benzoxazole 22 as a potent and selective VEGFR-2 inhibitor displaying a good pharmacokinetic profile. Compound 22 demonstrated efficacy in both the murine matrigel model for vascular permeability (79% inhibition observed at 100 mg/kg) and the rat corneal angiogenesis model (ED(50) = 16.3 mg/kg).

  • Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, USA. michelep@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): 5 
Gene Names: KDRFLK1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
GTEx:  ENSG00000128052 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35968
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 276

Download Ideal Coordinates CCD File 
B [auth A]4-[[2-[[4-chloro-3-(trifluoromethyl)phenyl]amino]-3H-benzimidazol-5-yl]oxy]-N-methyl-pyridine-2-carboxamide
C21 H15 Cl F3 N5 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Binding Affinity Annotations 
IDSourceBinding Affinity
276 BindingDB:  2QU5 Ki: 9 (nM) from 1 assay(s)
PDBBind:  2QU5 Ki: 8.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.852α = 90
b = 143.828β = 90
c = 58.483γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
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: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection