3EFL | pdb_00003efl

Crystal structure of the VEGFR2 kinase domain in complex with motesanib

• PDB DOI: https://doi.org/10.2210/pdb3EFL/pdb

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


• Deposited: 2008-09-09 Released: 2009-09-15 
• Deposition Author(s): Kim, J.L., Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.264 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.220 (DCC) 

Literature

Discovery of Motesanib

Tasker, A.S., Patel, V.F.

To be published.

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: 73.31 kDa 
• Atom Count: 4,623 
• Modeled Residue Count: 549 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A, B	314	Homo sapiens	Mutation(s): 2  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 GTEx:  ENSG00000128052

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
706	C [auth A], D [auth B]	N-(3,3-dimethyl-2,3-dihydro-1H-indol-6-yl)-2-[(pyridin-4-ylmethyl)amino]pyridine-3-carboxamide C22 H23 N5 O RAHBGWKEPAQNFF-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
706	BindingDB:  3EFL	Ki: 3 (nM) from 1 assay(s)
		Kd: 26 (nM) from 1 assay(s)
		IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.264 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.220 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.59	α = 90
b = 66.81	β = 93.27
c = 91.42	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Kim, J.L., Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

Revision History  

• Version 1.0: 2009-09-15
  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: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Structure summary