3BWJ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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This is version 1.4 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
  • Primary Citation of Related Structures:  
    3BWJ

  • 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 (ARC-type) inhibitors, was solved ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase, alpha-catalytic subunitA350Bos 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARX
Query on ARX
Download Ideal Coordinates CCD File 
B [auth A],
C [auth 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
C28 H47 N15 O7
KFJBBCJEBVHMMY-KRNUZZCISA-N		 Ligand Interaction
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
Binding Affinity Annotations 
IDSourceBinding Affinity
ARX Binding MOAD:  3BWJ Kd: 319 (nM) from 1 assay(s)
PDBBind:  3BWJ Kd: 319 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000645 (ARX)
Query on PRD_000645		B [auth A],
C [auth A]		ARC-1034Non-polymer / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.188α = 90
b = 72.632β = 90
c = 77.221γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

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: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2019-09-04
    Changes: Data collection, Derived calculations