6ILZ | pdb_00006ilz

Crystal structure of PKCiota in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free: 
    0.348 (Depositor), 0.350 (DCC) 
  • R-Value Work: 
    0.306 (Depositor), 0.310 (DCC) 
  • R-Value Observed: 
    0.310 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AFUClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Fragment-based Discovery of a Small-Molecule Protein Kinase C-iota Inhibitor Binding Post-kinase Domain Residues.

Kwiatkowski, J.Baburajendran, N.Poulsen, A.Liu, B.Tee, D.H.Y.Wong, Y.X.Poh, Z.Y.Ong, E.H.Dinie, N.Cherian, J.Jansson, A.E.Hill, J.Keller, T.H.Hung, A.W.

(2019) ACS Med Chem Lett 10: 318-323

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00546
  • Primary Citation of Related Structures:  
    6ILZ

  • PubMed Abstract: 

    The atypical protein kinase C-iota (PKC-ι) enzyme is implicated in various cancers and has been put forward as an attractive target for developing anticancer therapy. A high concentration biochemical screen identified pyridine fragment weakly inhibiting PKC-ι with IC 50 = 424 μM. Driven by structure-activity relationships and guided by docking hypothesis, the weakly bound fragment was eventually optimized into a potent inhibitor of PKC-ι (IC 50 = 270 nM). Through the course of the optimization, an intermediate compound was crystallized with the protein, and careful analysis of the X-ray crystal structure revealed a unique binding mode involving the post-kinase domain (C-terminal tail) of PKC-ι.


  • Organizational Affiliation

    Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase C iota typeA,
B [auth C],
C [auth E],
D [auth G]
345Homo sapiensMutation(s): 0 
Gene Names: PRKCIDXS1179E
EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for P41743 (Homo sapiens)
Explore P41743 
Go to UniProtKB:  P41743
PHAROS:  P41743
GTEx:  ENSG00000163558 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41743
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A,
B [auth C],
C [auth E],
D [auth G]
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
AFU BindingDB:  6ILZ IC50: 340 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free:  0.348 (Depositor), 0.350 (DCC) 
  • R-Value Work:  0.306 (Depositor), 0.310 (DCC) 
  • R-Value Observed: 0.310 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.87α = 90
b = 87.63β = 114.69
c = 105.181γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AFUClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary