2QU6 | pdb_00002qu6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.272 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.219 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2QU6

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

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 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

Macromolecule Content 

  • Total Structure Weight: 73.68 kDa 
  • Atom Count: 4,698 
  • Modeled Residue Count: 543 
  • Deposited Residue Count: 628 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2
A, B
314Homo sapiensMutation(s): 5 
Gene Names: KDRFLK1
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35968
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
857

Query on 857



Download:Ideal Coordinates CCD File
D [auth A],
E [auth B]
4-({2-[(4-chloro-3-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}phenyl)amino]-1,3-benzoxazol-5-yl}oxy)-N-methylpyridine-2-carboxamide
C26 H26 Cl N5 O4
KMNCFOUKJYOZIF-KRWDZBQOSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.272 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.219 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.37α = 90
b = 67.37β = 92.98
c = 89.62γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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: Source and taxonomy
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2024-02-21
    Changes: Data collection
  • Version 1.5: 2024-10-16
    Changes: Structure summary