3AG9

Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1012


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Diversity of bisubstrate binding modes of adenosine analogue-oligoarginine conjugates in protein kinase a and implications for protein substrate interactions.

Pflug, A.Rogozina, J.Lavogina, D.Enkvist, E.Uri, A.Engh, R.A.Bossemeyer, D.

(2010) J.Mol.Biol. 403: 66-77

  • DOI: 10.1016/j.jmb.2010.08.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of the catalytic subunit α of cAMP-dependent protein kinase (PKAc) with three adenosine analogue-oligoarginine conjugates (ARCs) are presented. The rationally designed ARCs include moieties that, in combination, target both the ATP ...

    Crystal structures of the catalytic subunit α of cAMP-dependent protein kinase (PKAc) with three adenosine analogue-oligoarginine conjugates (ARCs) are presented. The rationally designed ARCs include moieties that, in combination, target both the ATP- and the peptide-substrate-binding sites of PKAc, thereby taking advantage of high-affinity binding interactions offered by the ATP site while utilizing an additional mechanism for target specificity via binding to the peptide substrate site. The crystal structures demonstrate that, in accord with the previously reported bisubstrate character of ARCs, the inhibitors occupy both binding sites of PKAc. Further, they show new binding modes that may also apply to natural protein substrates of PKAc, which have not been revealed by previous crystallographic studies. The crystal structures described here contribute to the understanding of the substrate-binding patterns of PKAc and should also facilitate the design of inhibitors targeting PKAc and related protein kinases.


    Organizational Affiliation

    Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia. Electronic address: rogozina@ut.ee.,German Cancer Research Center, Group of Structural Biochemistry, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Electronic address: d.bossemeyer@dkfz-heidelberg.de.,Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia. Electronic address: darjalav@ut.ee.,Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway. Electronic address: alexander.pflug@uit.no.,Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia. Electronic address: erki.enkvist@ut.ee.,Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia. Electronic address: asko.uri@ut.ee.,Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway. Electronic address: Richard.Engh@uit.no.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
A, B
351Bos taurusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
Find proteins for P00517 (Bos taurus)
Go to Gene View: PRKACA
Go to UniProtKB:  P00517
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A02
Query on A02

Download SDF File 
Download CCD File 
B
(10R,20R,23R)-10-(4-aminobutyl)-1-[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-20,23-bis(3-carbamimidamidopropyl)-1,8,11,18,21-pentaoxo-2,9,12,19,22-pentaazatetracosan-24-amide
ARC-1012
C40 H70 N18 O9
LIYNJKNSBUCWCZ-SAPGASOESA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000641 (A02)
Query on PRD_000641
BINHIBITOR ARC-1012Non-polymer / Inhibitor

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Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A02Ki: 9 nM BINDINGMOAD
A02Ki: 9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.680α = 90.00
b = 88.040β = 90.00
c = 115.070γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Type: Other