3BE2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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: 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2A314Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAJ (Subject of Investigation/LOI)
Query on RAJ

Download Ideal Coordinates CCD File 
B [auth A]N-{3-[3-(DIMETHYLAMINO)PROPYL]-5-(TRIFLUOROMETHYL)PHENYL}-4-METHYL-3-[(3-PYRIMIDIN-4-YLPYRIDIN-2-YL)AMINO]BENZAMIDE
C29 H29 F3 N6 O
OHHGYJBFPVJURR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
RAJ Binding MOAD:  3BE2 IC50: 2 (nM) from 1 assay(s)
BindingDB:  3BE2 IC50: 2 (nM) from 1 assay(s)
PDBBind:  3BE2 IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.77α = 90
b = 84.38β = 100.09
c = 47.57γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations