8SF8

Structure of bovine PKA bound to (R)-N-(4-(1H-pyrrolo[2,3-b]pyridin-4-yl)phenyl)-2-amino-4-methylpentanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Characterization of Selective, First-in-Class Inhibitors of Citron Kinase.

Maw, J.J.Coker, J.A.Arya, T.Goins, C.M.Sonawane, D.Han, S.H.Rees, M.G.Ronan, M.M.Roth, J.A.Wang, N.S.Heemers, H.V.Macdonald, J.D.Stauffer, S.R.

(2024) J Med Chem 67: 2631-2666

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01807
  • Primary Citation of Related Structures:  
    8SF8

  • PubMed Abstract: 

    Citron kinase (CITK) is an AGC-family serine/threonine kinase that regulates cytokinesis. Despite knockdown experiments implicating CITK as an anticancer target, no selective CITK inhibitors exist. We transformed a previously reported kinase inhibitor with weak off-target CITK activity into a first-in-class CITK chemical probe, C3TD879 . C3TD879 is a Type I kinase inhibitor which potently inhibits CITK catalytic activity (biochemical IC 50 = 12 nM), binds directly to full-length human CITK in cells (NanoBRET K d < 10 nM), and demonstrates favorable DMPK properties for in vivo evaluation. We engineered exquisite selectivity for CITK (>17-fold versus 373 other human kinases), making C3TD879 the first chemical probe suitable for interrogating the complex biology of CITK. Our small-molecule CITK inhibitors could not phenocopy the effects of CITK knockdown in cell proliferation, cell cycle progression, or cytokinesis assays, providing preliminary evidence that the structural roles of CITK may be more important than its kinase activity.


  • Organizational Affiliation

    Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alpha353Bos taurusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus)
Explore P00517 
Go to UniProtKB:  P00517
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00517
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor alpha20Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3SX13 (Bos taurus)
Explore Q3SX13 
Go to UniProtKB:  Q3SX13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3SX13
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZWG (Subject of Investigation/LOI)
Query on ZWG

Download Ideal Coordinates CCD File 
C [auth A]N-[4-(1H-pyrrolo[2,3-b]pyridin-4-yl)phenyl]-D-leucinamide
C19 H22 N4 O
DQDRFKODMABANK-QGZVFWFLSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.653α = 90
b = 75.636β = 90
c = 80.652γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references