3LCD Transferase date Jan 10, 2010
title Inhibitor Bound To A Dfg-In Structure Of The Kinase Domain O
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, Fms Proto-Oncogene, C-Fms
Ec: 2.7.10.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Csf-1r, Csf1r, Fms
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.649 74.125 91.024 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand BDY, SO4 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):1543-1547. Epub 2010 Jan 21. PMID:20137931
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (3lcd.pdb1.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 3LCD
  • CSU: Contacts of Structural Units for 3LCD
  • Structure Factors (206 Kb)
  • Retrieve 3LCD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LCD from S2C, [Save to disk]
  • Re-refined 3lcd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LCD 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 3LCD
  • 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 3LCD, from MSDmotif at EBI
  • Fold representative 3lcd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lcd] [3lcd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LCD: [TyrKc ] by SMART
  • Other resources with information on 3LCD
  • Community annotation for 3LCD 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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