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 5EW3 | pdb_00005ew3

Human Vascular Endothelial Growth Factor Receptor 2 (KDR) Kinase Domain in complex with AAL993


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.254 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5EW3

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

A Novel Potent Oral Series of VEGFR2 Inhibitors Abrogate Tumor Growth by Inhibiting Angiogenesis.

Bold, G., Schnell, C., Furet, P., McSheehy, P., Bruggen, J., Mestan, J., Manley, P.W., Druckes, P., Burglin, M., Durler, U., Loretan, J., Reuter, R., Wartmann, M., Theuer, A., Bauer-Probst, B., Martiny-Baron, G., Allegrini, P., Goepfert, A., Wood, J., Littlewood-Evans, A.

(2016) J Med Chem 59: 132-146

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01582
  • Primary Citation Related Structures: 
    5EW3

  • PubMed Abstract: 

    This paper describes the identification of 6-(pyrimidin-4-yloxy)-naphthalene-1-carboxamides as a new class of potent and selective human vascular endothelial growth factor receptor 2 (VEGFR2) tyrosine kinase inhibitors. In biochemical and cellular assays, the compounds exhibit single-digit nanomolar potency toward VEGFR2. Compounds of this series show good exposure in rodents when dosed orally. They potently inhibit VEGF-driven angiogenesis in a chamber model and rodent tumor models at daily doses of less than 3 mg/kg by targeting the tumor vasculature as demonstrated by ELISA for TIE-2 in lysates or by immunohistochemical analysis. This novel series of compounds shows a potential for the treatment of solid tumors and other diseases where angiogenesis plays an important role.


  • Organizational Affiliation: 
    • Oncology Research, Novartis Institutes for BioMedical Research , 4002 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 73.13 kDa 
  • Atom Count: 4,453 
  • Modeled Residue Count: 540 
  • Deposited Residue Count: 632 
  • 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
316Homo sapiensMutation(s): 0 
Gene Names: KDR, FLK1, VEGFR2
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5T2

Query on 5T2



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
2-(pyridin-4-ylmethylamino)-~{N}-[3-(trifluoromethyl)phenyl]benzamide
C20 H16 F3 N3 O
BLAFVGLBBOPRLP-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5T2 BindingDB:  5EW3 IC50: min: 1.2, max: 170 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.254 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.5α = 90
b = 55.76β = 92.28
c = 89.76γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description