4HVS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.USA 110: 5689-5694

  • DOI: 10.1073/pnas.1219457110
  • Primary Citation of Related Structures:  

  • 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 th ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mast/stem cell growth factor receptor Kit
A
335Homo sapiensMutation(s): 18 
Gene Names: KIT (SCFR)
EC: 2.7.10.1
Find proteins for P10721 (Homo sapiens)
Go to Gene View: KIT
Go to UniProtKB:  P10721
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
647
Query on 647

Download SDF File 
Download CCD File 
A
5-(1H-pyrrolo[2,3-b]pyridin-3-ylmethyl)-N-[4-(trifluoromethyl)benzyl]pyridin-2-amine
C21 H17 F3 N4
NODCQQSEMCESEC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
647IC50: 16 nM BINDINGMOAD
647IC50: 16 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.735α = 90.00
b = 81.863β = 107.81
c = 50.055γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-11-06 
  • Released Date: 2013-03-27 
  • Deposition Author(s): Zhang, Y., Zhang, C.

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references