2RL5 Transferase date Oct 18, 2007
title Crystal Structure Of The Vegfr2 Kinase Domain In Complex Wit Dihydro-1,4-Benzoxazine Inhibitor
authors D.A.Whittington, A.M.Long, P.Rose, H.Zhao
compound source
Molecule: Vascular Endothelial Growth Factor Receptor 2
Chain: A
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_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 21 21 2
R_factor 0.199 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.760 139.774 57.550 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand 2RL BindingDB enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceNovel 2,3-dihydro-1,4-benzoxazines as potent and orally bioavailable inhibitors of tumor-driven angiogenesis., La DS, Belzile J, Bready JV, Coxon A, Demelfi T, Doerr N, Estrada J, Flynn JC, Flynn SR, Graceffa RF, Harriman SP, Larrow JF, Long AM, Martin MW, Morrison MJ, Patel VF, Roveto PM, Wang L, Weiss MM, Whittington DA, Teffera Y, Zhao Z, Polverino AJ, Harmange JC, J Med Chem. 2008 Mar 27;51(6):1695-705. Epub 2008 Feb 27. PMID:18311900
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (2rl5.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 2RL5
  • CSU: Contacts of Structural Units for 2RL5
  • Likely Quarternary Molecular Structure file(s) for 2RL5
  • Structure Factors (127 Kb)
  • Retrieve 2RL5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2RL5 from S2C, [Save to disk]
  • Re-refined 2rl5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2RL5 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 2RL5
  • 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 2RL5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2rl5_A] [2rl5]
  • SWISS-PROT database: [P35968]
  • Domain organization of [VGFR2_HUMAN] by SWISSPFAM
  • Domain found in 2RL5: [TyrKc ] by SMART
  • Other resources with information on 2RL5
  • Community annotation for 2RL5 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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