7MFC | pdb_00007mfc

Crystal structure of CSF1R in complex with vimseltinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.256 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7MFC

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Vimseltinib: A Precision CSF1R Therapy for Tenosynovial Giant Cell Tumors and Diseases Promoted by Macrophages.

Smith, B.D.Kaufman, M.D.Wise, S.C.Ahn, Y.M.Caldwell, T.M.Leary, C.B.Lu, W.P.Tan, G.Vogeti, L.Vogeti, S.Wilky, B.A.Davis, L.E.Sharma, M.Ruiz-Soto, R.Flynn, D.L.

(2021) Mol Cancer Ther 20: 2098-2109

  • DOI: https://doi.org/10.1158/1535-7163.MCT-21-0361
  • Primary Citation Related Structures: 
    7MFC

  • PubMed Abstract: 

    Macrophages can be co-opted to contribute to neoplastic, neurologic, and inflammatory diseases. Colony-stimulating factor 1 receptor (CSF1R)-dependent macrophages and other inflammatory cells can suppress the adaptive immune system in cancer and contribute to angiogenesis, tumor growth, and metastasis. CSF1R-expressing osteoclasts mediate bone degradation in osteolytic cancers and cancers that metastasize to bone. In the rare disease tenosynovial giant cell tumor (TGCT), aberrant CSF1 expression and production driven by a gene translocation leads to the recruitment and growth of tumors formed by CSF1R-dependent inflammatory cells. Small molecules and antibodies targeting the CSF1/CSF1R axis have shown promise in the treatment of TGCT and cancer, with pexidartinib recently receiving FDA approval for treatment of TGCT. Many small-molecule kinase inhibitors of CSF1R also inhibit the closely related kinases KIT, PDGFRA, PDGFRB, and FLT3, thus CSF1R suppression may be limited by off-target activity and associated adverse events. Vimseltinib (DCC-3014) is an oral, switch control tyrosine kinase inhibitor specifically designed to selectively and potently inhibit CSF1R by exploiting unique features of the switch control region that regulates kinase conformational activation. In preclinical studies, vimseltinib durably suppressed CSF1R activity in vitro and in vivo , depleted macrophages and other CSF1R-dependent cells, and resulted in inhibition of tumor growth and bone degradation in mouse cancer models. Translationally, in a phase I clinical study, vimseltinib treatment led to modulation of biomarkers of CSF1R inhibition and reduction in tumor burden in TGCT patients.


  • Organizational Affiliation
    • Deciphera Pharmaceuticals, LLC, Waltham, Massachusetts.

Macromolecule Content 

  • Total Structure Weight: 39.07 kDa 
  • Atom Count: 2,204 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 343 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptor343Homo sapiensMutation(s): 3 
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
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z6V
(Subject of Investigation/LOI)

Query on Z6V



Download:Ideal Coordinates CCD File
B [auth A]Vimseltinib
C23 H25 N7 O2
TVGAHWWPABTBCX-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Z6V BindingDB:  7MFC IC50: min: 2, max: 27 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.256 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.87α = 90
b = 61.87β = 90
c = 181.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description