2P2I Transferase date Mar 07, 2007
title Crystal Structure Of The Vegfr2 Kinase Domain In Complex Wit Nicotinamide Inhibitor
authors D.A.Whittington, J.L.Kim, A.M.Long, P.Rose, Y.Gu, H.Zhao
compound source
Molecule: Vascular Endothelial Growth Factor Receptor 2
Chain: A, B
Fragment: Kinase Domain
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 1 21 1
R_factor 0.222 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.420 67.060 88.510 90.00 94.51 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 608 BindingDB enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceEvolution of a highly selective and potent 2-(pyridin-2-yl)-1,3,5-triazine tie-2 kinase inhibitor., Hodous BL, Geuns-Meyer SD, Hughes PE, Albrecht BK, Bellon S, Bready J, Caenepeel S, Cee VJ, Chaffee SC, Coxon A, Emery M, Fretland J, Gallant P, Gu Y, Hoffman D, Johnson RE, Kendall R, Kim JL, Long AM, Morrison M, Olivieri PR, Patel VF, Polverino A, Rose P, Tempest P, Wang L, Whittington DA, Zhao H, J Med Chem. 2007 Feb 22;50(4):611-26. Epub 2007 Jan 25. PMID:17253678
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (2p2i.pdb1.gz) 50 Kb
  • Biological Unit Coordinates (2p2i.pdb2.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 2P2I
  • CSU: Contacts of Structural Units for 2P2I
  • Likely Quarternary Molecular Structure file(s) for 2P2I
  • Structure Factors (227 Kb)
  • Retrieve 2P2I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2P2I from S2C, [Save to disk]
  • Re-refined 2p2i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2P2I 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 2P2I
  • 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 2P2I, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2p2i_B] [2p2i_A] [2p2i]
  • SWISS-PROT database: [P35968]
  • Domain organization of [VGFR2_HUMAN] by SWISSPFAM
  • Domain found in 2P2I: [TyrKc ] by SMART
  • Other resources with information on 2P2I
  • Community annotation for 2P2I 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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