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 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    3DPK

  • 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 inflammatory diseases ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptor, Fibroblast growth factor receptor 1A335Homo sapiensMutation(s): 0 
Gene Names: CSF1R, FGFBR, FGFR1, FLG, FLT2, FMS, BFGFR, CEK, HBGFR
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11362 (Homo sapiens)
Explore P11362 
Go to UniProtKB:  P11362
PHAROS:  P11362
GTEx:  ENSG00000077782 
Find proteins for P07333 (Homo sapiens)
Explore P07333 
Go to UniProtKB:  P07333
PHAROS:  P07333
GTEx:  ENSG00000182578 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP11362P07333
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8C5
Query on 8C5
Download Ideal Coordinates CCD File 
E [auth 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
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
8C5 PDBBind:  3DPK IC50: 4.1 (nM) from 1 assay(s)
Binding MOAD:  3DPK IC50: 4.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.192 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.95α = 90
b = 80.95β = 90
c = 145.42γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

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