3DPK

cFMS tyrosine kinase in complex with a pyridopyrimidinone inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Pyrido[2,3-d]pyrimidin-5-ones: a novel class of antiinflammatory macrophage colony-stimulating factor-1 receptor inhibitors

Huang, H., Hutta, D.A., Rinker, J.M., Hu, H., Parsons, W.H., Schubert, C., DesJarlais, R.L., Crysler, C.S., Chaikin, M.A., Donatelli, R.R., Chen, Y., Cheng, D., Zhou, Z., Yurkow, E., Manthey, C.L., Player, M.R.

(2009) J.Med.Chem. 52: 1081-1099

  • DOI: 10.1021/jm801406h

  • PubMed Abstract: 

    • A series of pyrido[2,3-d]pyrimidin-5-ones has been synthesized and evaluated as inhibitors of the kinase domain of macrophage colony-stimulating factor-1 receptor (FMS). FMS inhibitors may be useful in treating rheumatoid arthritis and other chronic ...

    A series of pyrido[2,3-d]pyrimidin-5-ones has been synthesized and evaluated as inhibitors of the kinase domain of macrophage colony-stimulating factor-1 receptor (FMS). FMS inhibitors may be useful in treating rheumatoid arthritis and other chronic inflammatory diseases. Structure-based optimization of the lead amide analogue 10 led to hydroxamate analogue 37, which possessed excellent potency and an improved pharmacokinetic profile. During the chronic phase of streptococcal cell wall-induced arthritis in rats, compound 37 (10, 3, and 1 mg/kg) was highly effective at reversing established joint swelling. In an adjuvant-induced arthritis model in rats, 37 prevented joint swelling partially at 10 mg/kg. In this model, osteoclastogenesis and bone erosion were prevented by low doses (1 or 0.33 mg/kg) that had minimal impact on inflammation. These data underscore the potential of FMS inhibitors to prevent erosions and reduce symptoms in rheumatoid arthritis.

    Organizational Affiliation: 

    Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage colony-stimulating factor 1 receptor, Fibroblast growth factor receptor 1
A
335Homo sapiensMutation(s): 0 
Gene Names: FGFR1 (BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR), CSF1R (FMS)
EC: 2.7.10.1
Find proteins for P11362 (Homo sapiens)
Go to Gene View: FGFR1
Go to UniProtKB:  P11362
Find proteins for P07333 (Homo sapiens)
Go to Gene View: CSF1R
Go to UniProtKB:  P07333
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
8C5
Query on 8C5
Download SDF File 
Download CCD File 
A
8-cyclohexyl-N-methoxy-5-oxo-2-{[4-(2-pyrrolidin-1-ylethyl)phenyl]amino}-5,8-dihydropyrido[2,3-d]pyrimidine-6-carboxamide
C27 H34 N6 O3
LYINTIKJROJCGF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8C5IC50: 4.1 nM BINDINGMOAD
8C5IC50: 4.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 80.950α = 90.00
b = 80.950β = 90.00
c = 145.420γ = 120.00
Software Package:
Software NamePurpose
CNXphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-07-08 
  • Released Date: 2009-02-17 
  • Deposition Author(s): Schubert, C.

Revision History 

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-01-25
    Type: Database references, Source and taxonomy
  • Version 1.3: 2017-07-26
    Type: Source and taxonomy
  • Version 1.4: 2017-10-25
    Type: Refinement description