3LCO Transferase date Jan 11, 2010
title Inhibitor Bound To A Dfg-Out Structure Of The Kinase Domain
authors S.Kamtekar, J.E.Day, B.A.Reitz, K.J.Mathis, M.J.Meyers
compound source
Molecule: Macrophage Colony-Stimulating Factor 1 Receptor
Chain: A
Fragment: Kinase Domain
Synonym: Csf-1-R, Proto-Oncogene C-Fms
Ec: 2.7.10.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Csf-1r, Csf1r, Fms
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 43 21 2
R_factor 0.245 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.916 62.916 183.943 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand LC0 BindingDB enzyme Transferase E.C.2.7.10.1 BRENDA
Primary referenceStructure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode., Meyers MJ, Pelc M, Kamtekar S, Day J, Poda GI, Hall MK, Michener ML, Reitz BA, Mathis KJ, Pierce BS, Parikh MD, Mischke DA, Long SA, Parlow JJ, Anderson DR, Thorarensen A, Bioorg Med Chem Lett. 2010 Mar 1;20(5):1543-7. Epub 2010 Jan 21. PMID:20137931
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (3lco.pdb1.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 3LCO
  • CSU: Contacts of Structural Units for 3LCO
  • Structure Factors (83 Kb)
  • Retrieve 3LCO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LCO from S2C, [Save to disk]
  • Re-refined 3lco structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LCO 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 3LCO
  • 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 3LCO, from MSDmotif at EBI
  • Fold representative 3lco from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lco_A] [3lco]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LCO: [TyrKc ] by SMART
  • Other resources with information on 3LCO
  • Community annotation for 3LCO 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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