Crystal structure of KIT kinase domain with a small molecule inhibitor, PLX647

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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This is version 1.2 of the entry. See complete history


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
Mast/stem cell growth factor receptor Kit335Homo sapiensMutation(s): 18 
Gene Names: KITSCFR
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
GTEx:  ENSG00000157404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10721
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 647

Download Ideal Coordinates CCD File 
B [auth A]5-(1H-pyrrolo[2,3-b]pyridin-3-ylmethyl)-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine
C21 H17 F3 N4
Binding Affinity Annotations 
IDSourceBinding Affinity
647 Binding MOAD:  4HVS IC50: 16 (nM) from 1 assay(s)
PDBBind:  4HVS IC50: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.735α = 90
b = 81.863β = 107.81
c = 50.055γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

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: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description