3CP9 Transferase date Mar 31, 2008
title Crystal Structure Of The Vegfr2 Kinase Domain In Complex Wit Pyridone Inhibitor
authors D.A.Whittington, A.M.Long, P.Rose, Y.Gu, H.Zhao
compound source
Molecule: Vascular Endothelial Growth Factor Receptor 2
Chain: A, B
Fragment: Protein Kinase Domain, Residues 940-989 Deleted
Synonym: Vegfr-2, Kinase Insert Domain Receptor, Protein-Ty Kinase Receptor Flk-1, Cd309 Antigen;
Ec: 2.7.10.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdr, Flk1
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.570 67.170 89.102 90.00 93.08 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand C19 BindingDB enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDiscovery of Aryl Aminoquinazoline Pyridones as Potent, Selective, and Orally Efficacious Inhibitors of Receptor Tyrosine Kinase c-Kit., Hu E, Tasker A, White RD, Kunz RK, Human J, Chen N, Burli R, Hungate R, Novak P, Itano A, Zhang X, Yu V, Nguyen Y, Tudor Y, Plant M, Flynn S, Xu Y, Meagher KL, Whittington DA, Ng GY, J Med Chem. 2008 Jun 12;51(11):3065-8. Epub 2008 May 1. PMID:18447379
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (3cp9.pdb1.gz) 50 Kb
  • Biological Unit Coordinates (3cp9.pdb2.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 3CP9
  • CSU: Contacts of Structural Units for 3CP9
  • Likely Quarternary Molecular Structure file(s) for 3CP9
  • Structure Factors (172 Kb)
  • Retrieve 3CP9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CP9 from S2C, [Save to disk]
  • Re-refined 3cp9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CP9 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3CP9
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3CP9, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cp9] [3cp9_A] [3cp9_B]
  • SWISS-PROT database: [P35968]
  • Domain organization of [VGFR2_HUMAN] by SWISSPFAM
  • Domain found in 3CP9: [TyrKc ] by SMART
  • Other resources with information on 3CP9
  • Community annotation for 3CP9 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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