5IZJ

Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1411

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Literature

Bifunctional Ligands for Inhibition of Tight-Binding Protein-Protein Interactions.

Ivan, T., Enkvist, E., Viira, B., Manoharan, G.B., Raidaru, G., Pflug, A., Alam, K.A., Zaccolo, M., Engh, R.A., Uri, A.

(2016) Bioconjug Chem 27: 1900-1910

  • DOI: 10.1021/acs.bioconjchem.6b00293
  • Primary Citation of Related Structures:  
    5IZF, 5IZJ, 5J5X

  • PubMed Abstract: 

    • The acknowledged potential of small-molecule therapeutics targeting disease-related protein-protein interactions (PPIs) has promoted active research in this field. The strategy of using small molecule inhibitors (SMIs) to fight strong (tight-binding) PPIs tends to fall short due to the flat and wide interfaces of PPIs ...

    The acknowledged potential of small-molecule therapeutics targeting disease-related protein-protein interactions (PPIs) has promoted active research in this field. The strategy of using small molecule inhibitors (SMIs) to fight strong (tight-binding) PPIs tends to fall short due to the flat and wide interfaces of PPIs. Here we propose a biligand approach for disruption of strong PPIs. The potential of this approach was realized for disruption of the tight-binding (KD = 100 pM) tetrameric holoenzyme of cAMP-dependent protein kinase (PKA). Supported by X-ray analysis of cocrystals, bifunctional inhibitors (ARC-inhibitors) were constructed that simultaneously associated with both the ATP-pocket and the PPI interface area of the catalytic subunit of PKA (PKAc). Bifunctional inhibitor ARC-1411, possessing a KD value of 3 pM toward PKAc, induced the dissociation of the PKA holoenzyme with a low-nanomolar IC50, whereas the ATP-competitive inhibitor H89 bound to the PKA holoenzyme without disruption of the protein tetramer.

    Organizational Affiliation: 

    Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaA, B351Homo sapiensMutation(s): 0 
Gene Names: PRKACA, PKACA
EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens)
Explore P17612 
Go to UniProtKB:  P17612
PHAROS:  P17612
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17612
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
47P-AZ1-DAR-DARC [auth G]5Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
47P-AZ1-DAR-DAR-DARD [auth F]6Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6J9
Query on 6J9
Download Ideal Coordinates CCD File 
EA [auth B],
R [auth A]		4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine
C10 H13 N5
LZSXQBNNRGZPES-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
F [auth A],
FA [auth F],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.94α = 90
b = 84.99β = 90.09
c = 77.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 2.0: 2019-06-19
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary