3DPK Transferase date Jul 08, 2008
title Cfms Tyrosine Kinase In Complex With A Pyridopyrimidinone Inhibitor
authors C.Schubert
compound source
Molecule: Macrophage Colony-Stimulating Factor 1 Receptor
Chain: A
Fragment: Kinase Domain
Synonym: Csf-1-R, Fms Proto-Oncogene, C-Fms, Cd115 Antigen, Fgfr-1, Bfgf-R, Fms-Like Tyrosine Kinase 2, C-Fgr, Cd331 Antige;
Ec: 2.7.10.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Csf1r, Fms, Fgfr1, Fgfbr, Flg, Flt2
Expression_system: Spodoptera Frugiperda
symmetry Space Group: H 3
R_factor 0.186 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.950 80.950 145.420 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.95 Å
ligand 8C5, SO4 enzyme Transferase E.C.2.7.10.1 BRENDA
Primary referencePyrido[2,3-d]pyrimidin-5-ones: A Novel Class of Antiinflammatory Macrophage Colony-Stimulating Factor-1 Receptor Inhibitors (dagger)., Huang H, Hutta DA, Rinker JM, Hu H, Parsons WH, Schubert C, Desjarlais RL, Crysler CS, Chaikin MA, Donatelli RR, Chen Y, Cheng D, Zhou Z, Yurkow E, Manthey CL, Player MR, J Med Chem. 2009 Feb 4. PMID:19193011
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (3dpk.pdb1.gz) 92 Kb
  • LPC: Ligand-Protein Contacts for 3DPK
  • CSU: Contacts of Structural Units for 3DPK
  • Likely Quarternary Molecular Structure file(s) for 3DPK
  • Structure Factors (207 Kb)
  • Retrieve 3DPK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DPK from S2C, [Save to disk]
  • Re-refined 3dpk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DPK 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 3DPK
  • 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 3DPK, from MSDmotif at EBI
  • Fold representative 3dpk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dpk_A] [3dpk]
  • SWISS-PROT database: [P07333]
  • Domain organization of [CSF1R_HUMAN] by SWISSPFAM
  • Domain found in 3DPK: [TyrKc ] by SMART
  • Other resources with information on 3DPK
  • Community annotation for 3DPK 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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