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 Diffraction	resolution	1.95 Å
ligand	8C5, SO4	enzyme	Transferase E.C.2.7.10.1 BRENDA
Primary reference	Pyrido[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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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] SWISS-PROT database: [P07333] Domain organization of [CSF1R_HUMAN] by SWISSPFAM Domain found in 3DPK: [TyrKc ] by SMART Alignments of the sequence of 3DPK with the sequences similar proteins can be viewed for 3DPK's classification [CSF1R_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [CSF1R_HUMAN] at ProtoMap. Click on the Cluster number.

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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