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



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