3ewh Summary

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Crystal structure of the VEGFR2 kinase domain in complex with a pyridyl-pyrimidine benzimidazole inhibitor

The structure was published by Cee, V.J., Cheng, A.C., Romero, K., et al., Zhou, Y., Hughes, P., and Geuns-Meyer, S., in 2009 in a paper entitled "Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.6 Å and deposited in 2008.

The experimental data on which the structure is based was also deposited.

The PDB entry contains the structure of vascular endothelial growth factor receptor 2. This molecule has the UniProt identifier P35968 (VGFR2_HUMAN)search. The sample contained 314 residues which is < 90% of the natural sequence. Out of 314 residues 300 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule is most likely monomeric.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A vascular endothelial growth factor receptor 2 P35968 (815-1171) (VGFR2_HUMAN)search Homo sapienssearch < 90% 314 95%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P35968 (815 - 1171) vascular endothelial growth factor receptor 2 Homo sapiens

Chain Structural classification (CATH) Sequence family (Pfam)
A Phosphorylase Kinase; domain 1search, Transferase(Phosphotransferase) domain 1search Protein tyrosine kinasesearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A (P35968) ATP bindingsearch growth factor bindingsearch protein tyrosine kinase activitysearch protein kinase activitysearch transferase activity, transferring phosphorus-containing groupssearch vascular endothelial growth factor-activated receptor activitysearch transmembrane receptor protein tyrosine kinase activitysearch protein phosphorylationsearch vascular endothelial growth factor receptor signaling pathwaysearch transmembrane receptor protein tyrosine kinase signaling pathwaysearch integral component of membranesearch membranesearch

Chain InterPro annotation
A Protein kinase domainsearch Serine-threonine/tyrosine-protein kinase catalytic domainsearch Tyrosine-protein kinase, receptor class III, conserved sitesearch Tyrosine-protein kinase, active sitesearch Vascular endothelial growth factor receptor 2 (VEGFR2)search Protein kinase-like domainsearch Protein kinase, ATP binding sitesearch Tyrosine-protein kinase, catalytic domainsearch