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

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.218 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Naphthamides as Novel and Potent Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitors: Design, Synthesis and Evaluation

Harmange, J.C.Weiss, M.M.Germain, J.Polverino, A.J.Borg, G.Bready, J.Chen, D.Choquette, D.Coxon, A.DeMelfi, T.DiPietro, L.Doerr, N.Estrada, J.Flynn, J.Graceffa, R.F.Harriman, S.P.Kaufman, S.La, D.S.Long, A.Martin, M.W.Neervannan, S.Patel, V.F.Potashman, M.Regal, K.Roveto, P.M.Schrag, M.L.Starnes, C.Tasker, A.Teffera, Y.Wang, L.White, R.D.Whittington, D.A.Zanon, R.

(2008) J Med Chem 51: 1649-1667

  • DOI: https://doi.org/10.1021/jm701097z
  • Primary Citation of Related Structures:  
    3B8Q, 3BE2

  • PubMed Abstract: 

    A series of naphthyl-based compounds were synthesized as potential inhibitors of vascular endothelial growth factor (VEGF) receptors. Investigations of structure-activity relationships led to the identification of a series of naphthamides that are potent inhibitors of the VEGF receptor tyrosine kinase family. Numerous analogues demonstrated low nanomolar inhibition of VEGF-dependent human umbilical vein endothelial cell (HUVEC) proliferation, and of these several compounds possessed favorable pharmacokinetic (PK) profiles. In particular, compound 48 demonstrated significant antitumor efficacy against established HT29 human colon adenocarcinoma xenografts implanted in athymic mice. A full account of the preparation, structure-activity relationships, pharmacokinetic properties, and pharmacology of analogues within this series is presented.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2
A, B
314Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 900

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C28 H21 Cl N2 O4
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
900 PDBBind:  3B8Q IC50: 0.5 (nM) from 1 assay(s)
BindingDB:  3B8Q IC50: min: 0.03, max: 0.5 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.116α = 90
b = 67.782β = 92.137
c = 88.089γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-23
    Changes: Source and taxonomy
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection