6ILZ

Crystal structure of PKCiota in complex with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.310 

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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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Protein kinase C iota typeA,
B [auth C],
C [auth E],
D [auth G]		345Homo sapiensMutation(s): 0 
Gene Names: PRKCI, DXS1179E
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AFU
Query on AFU
Download Ideal Coordinates CCD File 
E [auth A],
F [auth C],
G [auth E],
H [auth G]		2-amino-5-[3-(piperazin-1-yl)phenyl]-N-(pyridin-4-yl)pyridine-3-carboxamide
C21 H22 N6 O
YDMJAALVMGFGRY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		A,
B [auth C],
C [auth E],
D [auth G]		L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.310 
  • 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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release