3BWJ

Complex of PKA with the bisubstrate protein kinase inhibitor lead compound Arc-1034


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural analysis of ARC-type inhibitor (ARC-1034) binding to protein kinase A catalytic subunit and rational design of bisubstrate analogue inhibitors of basophilic protein kinases.

Lavogina, D.Lust, M.Viil, I.Konig, N.Raidaru, G.Rogozina, J.Enkvist, E.Uri, A.Bossemeyer, D.

(2009) J.Med.Chem. 52: 308-321

  • DOI: 10.1021/jm800797n

  • PubMed Abstract: 
  • The crystal structure of a complex of the catalytic subunit (type alpha) of cAMP-dependent protein kinase (PKA C alpha) with ARC-type inhibitor (ARC-1034), the presumed lead scaffold of previously reported adenosine-oligo-arginine conjugate-based (AR ...

    The crystal structure of a complex of the catalytic subunit (type alpha) of cAMP-dependent protein kinase (PKA C alpha) with ARC-type inhibitor (ARC-1034), the presumed lead scaffold of previously reported adenosine-oligo-arginine conjugate-based (ARC-type) inhibitors, was solved. Structural elements important for interaction with the kinase were established with specifically modified derivatives of the lead compound. On the basis of this knowledge, a new generation of inhibitors, conjugates of adenosine-4'-dehydroxymethyl-4'-carboxylic acid moiety and oligo(D-arginine), was developed with inhibitory constants well into the subnanomolar range. The structural determinants of selectivity of the new compounds were established in assays with ROCK-II and PKBgamma.


    Related Citations: 
    • Conjugation of Adenosine and Hexa-(D-arginine)Leads to a Nanomolar Bisubstrate-Analog Inhibitor of Basophilic Protein Kinases
      Enkvist, E.,Lavogina, D.,Raidaru, G.,Vaasa, A.,Viil, I.,Lust, M.,Viht, K.,Uri, A.
      (2006) J.Med.Chem. 49: 7150


    Organizational Affiliation

    Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase, alpha-catalytic subunit
A
350Bos 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
ARX
Query on ARX

Download SDF File 
Download CCD File 
A
(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-N-(6-{[(1R)-4-carbamimidamido-1-{[(1R)-4-carbamimidamido-1-carbamoylbutyl]carbamoyl}butyl]amino}-6-oxohexyl)-3,4-dihydroxytetrahydrofuran-2-carboxamide
ARC-1034
C28 H47 N15 O7
KFJBBCJEBVHMMY-KRNUZZCISA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000645 (ARX)
Query on PRD_000645
AARC-1034Non-polymer / Inhibitor

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Modified Residues  2 Unique
IDChainsTypeFormula2D 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ARXIC50: 2600 nM BINDINGMOAD
ARXKd: 319 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.188α = 90.00
b = 72.632β = 90.00
c = 77.221γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-03
    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
  • Version 1.3: 2017-10-25
    Type: Refinement description