3C7Q Transferase date Feb 08, 2008
title Structure Of Vegfr2 Kinase Domain In Complex With Bibf1120
authors F.Hilberg, G.J.Roth, M.Krssak, S.Kautschitsch, W.Sommergruber, U. Grunt, P.Garin-Chesa, G.Bader, A.Zoephel, J.Quant, A.Heckel, W.J.
compound source
Molecule: Vascular Endothelial Growth Factor Receptor 2
Chain: A
Fragment: Kinase Domain
Synonym: Vegfr-2, Kinase Insert Domain Receptor, Protein-Ty Kinase Receptor Flk-1, Cd309 Antigen;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdr, Flk1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: High5
Expression_system_cell_line: Sf9
Expression_system_vector_type: Vector
Expression_system_vector: Pfb1
symmetry Space Group: P 21 21 21
R_factor 0.217 R_Free 0.279
length a length b length c angle alpha angle beta angle gamma
38.250 94.440 96.220 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CME, PTR, SO4, XIN BindingDB enzyme Transferase E.C. BRENDA

Primary referenceBIBF 1120: triple angiokinase inhibitor with sustained receptor blockade and good antitumor efficacy., Hilberg F, Roth GJ, Krssak M, Kautschitsch S, Sommergruber W, Tontsch-Grunt U, Garin-Chesa P, Bader G, Zoephel A, Quant J, Heckel A, Rettig WJ, Cancer Res. 2008 Jun 15;68(12):4774-82. PMID:18559524
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (3c7q.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 3C7Q
  • CSU: Contacts of Structural Units for 3C7Q
  • Structure Factors (159 Kb)
  • Retrieve 3C7Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C7Q from S2C, [Save to disk]
  • Re-refined 3c7q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C7Q 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 3C7Q
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3C7Q, from MSDmotif at EBI
  • Fold representative 3c7q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c7q] [3c7q_A]
  • SWISS-PROT database: [P35968]
  • Domain organization of [VGFR2_HUMAN] by SWISSPFAM
  • Domain found in 3C7Q: [TyrKc ] by SMART
  • Other resources with information on 3C7Q
  • Community annotation for 3C7Q 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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