4R7I

Crystal structure of FMS kinase domain with a small molecular inhibitor, GLEEVEC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1056/NEJMoa1411366
  • Primary Citation of Related Structures:  

  • 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).

    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.).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage colony-stimulating factor 1 receptor
A
343Homo sapiensMutation(s): 3 
Gene Names: CSF1R (FMS)
Find proteins for P07333 (Homo sapiens)
Go to Gene View: CSF1R
Go to UniProtKB:  P07333
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STI
Query on STI

Download SDF File 
Download CCD File 
A
4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE
STI-571;IMATINIB
C29 H31 N7 O
KTUFNOKKBVMGRW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
STIIC50: 291 - 1274 nM (86) BINDINGDB
STIKd: 11 - 19000 nM (86) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.130α = 90.00
b = 63.130β = 90.00
c = 183.460γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
SCALAdata scaling
MOSFLMdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-08-27 
  • Released Date: 2015-08-12 
  • Deposition Author(s): Zhang, Y., Zhang, C.

Revision History 

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