4E93 | pdb_00004e93

Crystal structure of human Feline Sarcoma Viral Oncogene Homologue (v-FES)in complex with TAE684


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.238 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.186 (Depositor) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4E93

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Small-Molecule Inhibitors of the c-Fes Protein-Tyrosine Kinase.

Hellwig, S.Miduturu, C.V.Kanda, S.Zhang, J.Filippakopoulos, P.Salah, E.Deng, X.Choi, H.G.Zhou, W.Hur, W.Knapp, S.Gray, N.S.Smithgall, T.E.

(2012) Chem Biol 19: 529-540

  • DOI: https://doi.org/10.1016/j.chembiol.2012.01.020
  • Primary Citation Related Structures: 
    4E93

  • PubMed Abstract: 

    The c-Fes protein-tyrosine kinase modulates cellular signaling pathways governing differentiation, the innate immune response, and vasculogenesis. Here, we report the identification of types I and II kinase inhibitors with potent activity against c-Fes both in vitro and in cell-based assays. One of the most potent inhibitors is the previously described anaplastic lymphoma kinase inhibitor TAE684. The crystal structure of TAE684 in complex with the c-Fes SH2-kinase domain showed excellent shape complementarity with the ATP-binding pocket and a key role for the gatekeeper methionine in the inhibitory mechanism. TAE684 and two pyrazolopyrimidines with nanomolar potency against c-Fes in vitro were used to establish a role for this kinase in osteoclastogenesis, illustrating the value of these inhibitors as tool compounds to probe the diverse biological functions associated with this unique kinase.


  • Organizational Affiliation
    • Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.

Macromolecule Content 

  • Total Structure Weight: 43.37 kDa 
  • Atom Count: 3,107 
  • Modeled Residue Count: 361 
  • Deposited Residue Count: 377 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase Fes/Fps377Homo sapiensMutation(s): 0 
Gene Names: FESFPS
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P07332 (Homo sapiens)
Explore P07332 
Go to UniProtKB:  P07332
PHAROS:  P07332
GTEx:  ENSG00000182511 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07332
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GUI

Query on GUI



Download:Ideal Coordinates CCD File
B [auth A]5-CHLORO-N-[2-METHOXY-4-[4-(4-METHYLPIPERAZIN-1-YL)PIPERIDIN-1-YL]PHENYL]-N'-(2-PROPAN-2-YLSULFONYLPHENYL)PYRIMIDINE-2,4-DIAMINE
C30 H40 Cl N7 O3 S
QQWUGDVOUVUTOY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GUI BindingDB:  4E93 Kd: 4.8 (nM) from 1 assay(s)
IC50: 569 (nM) from 1 assay(s)
EC50: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.238 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.186 (Depositor) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.97α = 90
b = 35.33β = 96.58
c = 100.72γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description