2XIR | pdb_00002xir

Crystal structure of the VEGFR2 kinase domain in complex with PF- 00337210 (N,2-dimethyl-6-(7-(2-morpholinoethoxy)quinolin-4-yloxy) benzofuran-3-carboxamide)

• PDB DOI: https://doi.org/10.2210/pdb2XIR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2010-06-30 Released: 2011-04-13 
• Deposition Author(s): McTigue, M., Wickersham, J., Pinko, C., Hong, Y., Marrone, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.238 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Discovery of the Selective Vegfr Inhibitor Pf- 00337210

Mctigue, M., Wickersham, J., Marrone, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.66 kDa 
• Atom Count: 2,709 
• Modeled Residue Count: 296 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2	A	316	Homo sapiens	Mutation(s): 1  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
00J	B [auth A]	N,2-DIMETHYL-6-{[7-(2-MORPHOLIN-4-YLETHOXY)QUINOLIN-4-YL]OXY}-1-BENZOFURAN-3-CARBOXAMIDE C26 H27 N3 O5 LGXVKMDGSIWEHL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.238 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.267	α = 90
b = 56.827	β = 94.18
c = 52.187	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-13 
Deposition Author(s): McTigue, M., Wickersham, J., Pinko, C., Hong, Y., Marrone, T.

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description