3BEA

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

• PDB DOI: https://doi.org/10.2210/pdb3BEA/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2007-11-16 Released: 2008-07-15 
• Deposition Author(s): Schubert, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.230 
• R-Value Work: 0.193 

Starting Model: experimental

Literature

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

• PubMed: 18342505 
• DOI: https://doi.org/10.1016/j.bmcl.2008.02.070
• Primary Citation of Related Structures:  
  3BEA


• 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%.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.45 kDa 
• Atom Count: 2,683 
• Modelled Residue Count: 310 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage colony-stimulating factor 1 receptor	A	333	Homo sapiens	Mutation(s): 1  Gene Names: CSF1R, FMS EC: 2.7.10.1
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
UniProt Groups	Q02763P07333

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IXH	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 AHBSXTVFKVCNCE-HDICACEKSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
IXH	PDBBind:  3BEA	IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.230 
• R-Value Work: 0.193 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.14	α = 90
b = 81.14	β = 90
c = 145.65	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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