Crystal structure of FMS kinase domain with a small molecular inhibitor, PLX647-OME

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

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Design and pharmacology of a highly specific dual FMS and KIT kinase inhibitor.

Zhang, C.Ibrahim, P.N.Zhang, J.Burton, E.A.Habets, G.Zhang, Y.Powell, B.West, B.L.Matusow, B.Tsang, G.Shellooe, R.Carias, H.Nguyen, H.Marimuthu, A.Zhang, K.Y.Oh, A.Bremer, R.Hurt, C.R.Artis, D.R.Wu, G.Nespi, M.Spevak, W.Lin, P.Nolop, K.Hirth, P.Tesch, G.H.Bollag, G.

(2013) Proc Natl Acad Sci U S A 110: 5689-5694

  • DOI: https://doi.org/10.1073/pnas.1219457110
  • Primary Citation of Related Structures:  
    4HVS, 4HW7

  • PubMed Abstract: 

    Inflammation and cancer, two therapeutic areas historically addressed by separate drug discovery efforts, are now coupled in treatment approaches by a growing understanding of the dynamic molecular dialogues between immune and cancer cells. Agents that target specific compartments of the immune system, therefore, not only bring new disease modifying modalities to inflammatory diseases, but also offer a new avenue to cancer therapy by disrupting immune components of the microenvironment that foster tumor growth, progression, immune evasion, and treatment resistance. McDonough feline sarcoma viral (v-fms) oncogene homolog (FMS) and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) are two hematopoietic cell surface receptors that regulate the development and function of macrophages and mast cells, respectively. We disclose a highly specific dual FMS and KIT kinase inhibitor developed from a multifaceted chemical scaffold. As expected, this inhibitor blocks the activation of macrophages, osteoclasts, and mast cells controlled by these two receptors. More importantly, the dual FMS and KIT inhibition profile has translated into a combination of benefits in preclinical disease models of inflammation and cancer.

  • Organizational Affiliation

    Plexxikon Inc., Berkeley, CA 94710, USA. CZhang@plexxikon.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptor343Homo 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
GTEx:  ENSG00000182578 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07333
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 64M

Download Ideal Coordinates CCD File 
B [auth A]5-[(5-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine
C22 H19 F3 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
64M PDBBind:  4HW7 IC50: 62 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.964α = 90
b = 62.964β = 90
c = 182.78γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
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: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations