4DBN Transferase Transferase Inhibitor date Jan 16, 2012
title Crystal Structure Of The Kinase Domain Of Human B-Raf With A 3]Thiazolo[5,4-B]Pyridine Derivative
authors J.K.Yano, K.Aertgeerts
compound source
Molecule: Serinethreonine-Protein Kinase B-Raf
Chain: A, B
Fragment: Kinase Domain (Unp Residues 445-726)
Synonym: Proto-Oncogene B-Raf, P94, V-Raf Murine Sarcoma Vi Oncogene Homolog B1;
Ec: 2.7.11.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Braf, Braf1, P94, Rafb1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 41 21 2
R_factor 0.196 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.040 111.040 146.844 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.15 Å
ligand 0JA enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDesign and Synthesis of Novel DFG-Out RAF/Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) Inhibitors. 1. Exploration of [5,6]-Fused Bicyclic Scaffolds., Okaniwa M, Hirose M, Imada T, Ohashi T, Hayashi Y, Miyazaki T, Arita T, Yabuki M, Kakoi K, Kato J, Takagi T, Kawamoto T, Yao S, Sumita A, Tsutsumi S, Tottori T, Oki H, Sang BC, Yano J, Aertgeerts K, Yoshida S, Ishikawa T, J Med Chem. 2012 Mar 14. PMID:22376051
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (186 Kb) [Save to disk]
  • Biological Unit Coordinates (4dbn.pdb1.gz) 180 Kb
  • Biological Unit Coordinates (4dbn.pdb2.gz) 91 Kb
  • Biological Unit Coordinates (4dbn.pdb3.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 4DBN
  • CSU: Contacts of Structural Units for 4DBN
  • Structure Factors (254 Kb)
  • Retrieve 4DBN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DBN from S2C, [Save to disk]
  • Re-refined 4dbn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DBN 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 4DBN
  • 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 4DBN, from MSDmotif at EBI
  • Fold representative 4dbn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dbn] [4dbn_B] [4dbn_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DBN: [STYKc ] by SMART
  • Other resources with information on 4DBN
  • Community annotation for 4DBN at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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