1YWN

Vegfr2 in complex with a novel 4-amino-furo[2,3-d]pyrimidine

• PDB DOI: https://doi.org/10.2210/pdb1YWN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2005-02-18 Released: 2005-08-23 
• Deposition Author(s): Miyazaki, Y., Matsunaga, S., Tang, J., Maeda, Y., Nakano, M., Philippe, R.J., Shibahara, M., Liu, W., Sato, H., Wang, L., Nolte, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Novel 4-amino-furo[2,3-d]pyrimidines as Tie-2 and VEGFR2 dual inhibitors

Miyazaki, Y., Matsunaga, S., Tang, J., Maeda, Y., Nakano, M., Philippe, R.J., Shibahara, M., Liu, W., Sato, H., Wang, L., Nolte, R.T.

(2005) Bioorg Med Chem Lett 15: 2203-2207

• PubMed: 15837294 
• DOI: https://doi.org/10.1016/j.bmcl.2005.03.034
• Primary Citation of Related Structures:  
  1YWN


• PubMed Abstract: 
  

  A novel class of furo[2,3-d]pyrimidines has been discovered as potent dual inhibitors of Tie-2 and VEGFR2 receptor tyrosine kinases (TK) and a diarylurea moiety at 5-position shows remarkably enhanced activity against both enzymes. One of the most active compounds, 4-amino-3-(4-((2-fluoro-5-(trifluoromethyl)phenyl)amino-carbonylamino)phenyl)-2-(4-methoxyphenyl)furo[2,3-d]pyrimidine (7k) is <3 nM on both TK receptors and the activity is rationalized based on the X-ray crystal structure.

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Organizational Affiliation: 

GlaxoSmithKline K.K., Tsukuba Research Laboratories, 43, Wadai, Tsukuba 300-4247, Ibaraki, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.89 kDa 
• Atom Count: 2,512 
• Modelled Residue Count: 281 
• 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): 3  Gene Names: KDR, FLK1 EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
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
LIF	B [auth A]	N-{4-[4-AMINO-6-(4-METHOXYPHENYL)FURO[2,3-D]PYRIMIDIN-5-YL]PHENYL}-N'-[2-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]UREA C27 H19 F4 N5 O3 FGZIONRFHVNRJB-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
LIF	BindingDB:  1YWN	IC50: min: 3, max: 15.49 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.953	α = 90
b = 95.595	β = 90
c = 95.803	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-23 
Deposition Author(s): Miyazaki, Y., Matsunaga, S., Tang, J., Maeda, Y., Nakano, M., Philippe, R.J., Shibahara, M., Liu, W., Sato, H., Wang, L., Nolte, R.T.

Revision History  

• Version 1.0: 2005-08-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.6: 2023-11-15
  Changes: Data collection
• Version 1.7: 2024-10-16
  Changes: Structure summary