8W1L | pdb_00008w1l

Structure of CSF1R kinase domain in complex with Cpd 32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Identification of Selective Imidazopyridine CSF1R Inhibitors.

Kane Jr., J.L.Asmussen, G.Batchelor, J.Cromwell, M.Fezoui, M.Fitzgerald, M.Giese, B.Gladysheva, T.Holley, S.Keefe, K.Kothe, M.Lam, B.Lim, S.Liu, J.Ma, L.Metz, M.Scholte, A.A.Shum, P.Wei, L.Woodworth, L.Edling, A.

(2024) ACS Med Chem Lett 15: 722-730

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00110
  • Primary Citation Related Structures: 
    8W1L

  • PubMed Abstract: 

    Colony stimulating factor-1 receptor (CSF1R or c-FMS), a class III receptor tyrosine kinase expressed on members of the mononuclear phagocyte system (MPS), plays a key role in the proper functioning of macrophages, microglia, and related cells. Aberrant signaling through CSF1R has been associated with a variety of disease states, including cancer, inflammation, and neurodegeneration. In this Letter, we detail our efforts to develop novel CSF1R inhibitors. Drawing on previously described compounds, including GW2580 ( 4 ), we have discovered a novel series of compounds based on the imidazo[4,5- b ]pyridine scaffold. Initial structure-activity relationship studies culminated in the identification of 36 , a lead compound with potent CSF1R biochemical and cellular activity, acceptable in vitro ADME properties, and oral exposure in rat.


  • Organizational Affiliation
    • Integrated Drug Discovery, Sanofi R&D, 350 Water Street, Cambridge, Massachusetts 02141, United States.

Macromolecule Content 

  • Total Structure Weight: 38.64 kDa 
  • Atom Count: 2,262 
  • Modeled Residue Count: 282 
  • Deposited Residue Count: 333 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptor,CSF1R333Homo sapiensMutation(s): 0 
Gene Names: CSF1RFMS
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
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 GroupP07333
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.02α = 90
b = 81.02β = 90
c = 146.06γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release