4KSP Transferase Transferase Inhibitor date May 17, 2013
title Crystal Structure Of Human B-Raf Bound To A Dfg-Out Inhibito
authors J.K.Yano, O.Masanori
compound source
Molecule: Serinethreonine-Protein Kinase B-Raf
Chain: A, B
Fragment: 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, V-Raf Murine Sarcoma Viral O Homolog B1;
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 41 21 2
R_factor 0.194 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.495 111.495 145.487 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.93 Å
ligand 1SU enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDiscovery of a Selective Kinase Inhibitor (TAK-632) Targeting Pan-RAF Inhibition: Design, Synthesis, and Biological Evaluation of C-7-Substituted 1,3-Benzothiazole Derivatives., Okaniwa M, Hirose M, Arita T, Yabuki M, Nakamura A, Takagi T, Kawamoto T, Uchiyama N, Sumita A, Tsutsumi S, Tottori T, Inui Y, Sang BC, Yano J, Aertgeerts K, Yoshida S, Ishikawa T, J Med Chem. 2013 Aug 22;56(16):6478-94. doi: 10.1021/jm400778d. Epub 2013 Aug 1. PMID:23906342
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (185 Kb) [Save to disk]
  • Biological Unit Coordinates (4ksp.pdb1.gz) 178 Kb
  • Biological Unit Coordinates (4ksp.pdb2.gz) 90 Kb
  • Biological Unit Coordinates (4ksp.pdb3.gz) 90 Kb
  • LPC: Ligand-Protein Contacts for 4KSP
  • CSU: Contacts of Structural Units for 4KSP
  • Structure Factors (452 Kb)
  • Retrieve 4KSP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KSP from S2C, [Save to disk]
  • Re-refined 4ksp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KSP 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 4KSP
  • 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 4KSP, from MSDmotif at EBI
  • Fold representative 4ksp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ksp_B] [4ksp] [4ksp_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4KSP: [STYKc ] by SMART
  • Other resources with information on 4KSP
  • Community annotation for 4KSP at PDBWiki (http://pdbwiki.org)

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