3EWH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.234 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.210 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted K11Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


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

  • 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


Macromolecules
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
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K11
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
VIHXUAKPZPXVSW-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
K11 BindingDB:  3EWH IC50: min: 69, max: 70 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
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
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted K11Click on this verticalbar to view details

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