Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.54 kDa 
• Atom Count: 4,662 
• Modelled Residue Count: 563 
• Deposited Residue Count: 628 
• Unique protein chains: 1

 3B8Q

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

• PDB DOI:  https://doi.org/10.2210/pdb3B8Q/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2007-11-01 Released: 2008-04-01 
• Deposition Author(s): Whittington, D.A., Long, A.M., Gu, Y., Zhao, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.276 
• R-Value Work: 0.218 

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

• PubMed: 18324761 
• 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.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Cambridge, MA 02139, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A, B	314	Homo sapiens	Mutation(s): 3  Gene Names: KDR, FLK1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
900	C [auth A], D [auth B]	N-(4-chlorophenyl)-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide C28 H21 Cl N2 O4 WUBFAXNVDMCVIO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
900	BindingDB:  3B8Q	IC50: min: 0.03, max: 0.5 (nM) from 4 assay(s)
	PDBBind:  3B8Q	IC50: 0.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 55.116	α = 90
b = 67.782	β = 92.137
c = 88.089	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Whittington, D.A., Long, A.M., Gu, Y., Zhao, H.

Revision History  

• 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