Crystal structure of FMS KINASE domain with a small molecular inhibitor, PLX3397

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 

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Structure-Guided Blockade of CSF1R Kinase in Tenosynovial Giant-Cell Tumor.

Tap, W.D.Wainberg, Z.A.Anthony, S.P.Ibrahim, P.N.Zhang, C.Healey, J.H.Chmielowski, B.Staddon, A.P.Cohn, A.L.Shapiro, G.I.Keedy, V.L.Singh, A.S.Puzanov, I.Kwak, E.L.Wagner, A.J.Von Hoff, D.D.Weiss, G.J.Ramanathan, R.K.Zhang, J.Habets, G.Zhang, Y.Burton, E.A.Visor, G.Sanftner, L.Severson, P.Nguyen, H.Kim, M.J.Marimuthu, A.Tsang, G.Shellooe, R.Gee, C.West, B.L.Hirth, P.Nolop, K.van de Rijn, M.Hsu, H.H.Peterfy, C.Lin, P.S.Tong-Starksen, S.Bollag, G.

(2015) N Engl J Med 373: 428-437

  • DOI: https://doi.org/10.1056/NEJMoa1411366
  • Primary Citation of Related Structures:  
    4R7H, 4R7I

  • PubMed Abstract: 
  • Expression of the colony-stimulating factor 1 (CSF1) gene is elevated in most tenosynovial giant-cell tumors. This observation has led to the discovery and clinical development of therapy targeting the CSF1 receptor (CSF1R).

    Organizational Affiliation

    From Memorial Sloan Kettering Cancer Center (W.D.T., J.H.H.) and Weill Cornell Medical College (W.D.T.) - both in New York; University of California, Los Angeles, Medical Center, Los Angeles (Z.A.W., B.C., A.S.S.), Plexxikon, Berkeley (P.N.I., C.Z., J.Z., G.H., Y.Z., E.A.B., G.V., L.S., P.S., H.N., M.J.K., A.M., G.T., R.S., C.G., B.L.W., P.H., K.N., H.H.H., P.S.L., S.T.-S., G.B.), and Stanford University School of Medicine, Stanford (M.R.) - all in California; Evergreen Hematology and Oncology, Spokane, WA (S.P.A.); University of Pennsylvania School of Medicine, Philadelphia (A.P.S.); Rocky Mountain Cancer Centers, Denver (A.L.C.); Dana-Farber Cancer Institute (G.I.S., A.J.W.) and Massachusetts General Hospital (E.L.K.) - both in Boston; Vanderbilt University Medical Center, Nashville (V.L.K., I.P.); Virginia G. Piper Cancer Center at Scottsdale Healthcare-Translational Genomics Research Institute (TGen), Scottsdale, AZ (D.D.V.H., G.J.W., R.K.R.); and Spire Sciences, Boca Raton, FL (C.P.).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptorA343Homo sapiensMutation(s): 3 
Gene Names: CSF1RFMS
UniProt & NIH Common Fund Data Resources
Find proteins for P07333 (Homo sapiens)
Explore P07333 
Go to UniProtKB:  P07333
PHAROS:  P07333
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07333
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on P31

Download Ideal Coordinates CCD File 
B [auth A]5-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-{[6-(trifluoromethyl)pyridin-3-yl]methyl}pyridin-2-amine
C20 H15 Cl F3 N5
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.984α = 90
b = 63.984β = 90
c = 185.041γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release