cFMS tyrosine kinase (tie2 KID) in complex with a pyrimidinopyridone inhibitor

Experimental Data Snapshot

  • Resolution: 2.02 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Design and synthesis of a pyrido[2,3-d]pyrimidin-5-one class of anti-inflammatory FMS inhibitors.

Huang, H.Hutta, D.A.Hu, H.DesJarlais, R.L.Schubert, C.Petrounia, I.P.Chaikin, M.A.Manthey, C.L.Player, M.R.

(2008) Bioorg Med Chem Lett 18: 2355-2361

  • DOI: https://doi.org/10.1016/j.bmcl.2008.02.070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A series of pyrimidinopyridones has been designed, synthesized and shown to be potent and selective inhibitors of the FMS tyrosine kinase. Introduction of an amide substituent at the 6-position of the pyridone core resulted in a significant potency increase. Compound 24 effectively inhibited in vivo LPS-induced TNF in mice greater than 80%.

  • Organizational Affiliation

    Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, PA 19477, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptor333Homo sapiensMutation(s): 1 
Gene Names: CSF1RFMS
UniProt & NIH Common Fund Data Resources
Find proteins for Q02763 (Homo sapiens)
Explore Q02763 
Go to UniProtKB:  Q02763
PHAROS:  Q02763
GTEx:  ENSG00000120156 
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 GroupsQ02763P07333
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IXH

Download Ideal Coordinates CCD File 
E [auth A]8-(2,3-dihydro-1H-inden-5-yl)-2-({4-[(3R,5S)-3,5-dimethylpiperazin-1-yl]phenyl}amino)-5-oxo-5,8-dihydropyrido[2,3-d]pyrimidine-6-carboxamide
C29 H31 N7 O2
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
IXH Binding MOAD:  3BEA IC50: 7 (nM) from 1 assay(s)
PDBBind:  3BEA IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.02 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.14α = 90
b = 81.14β = 90
c = 145.65γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2008-07-15 
  • Deposition Author(s): Schubert, C.

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Source and taxonomy
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description