4UJA

Protein Kinase A in complex with an Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Addressing the Glycine-Rich Loop of Protein Kinases by a Multi-Facetted Interaction Network: Inhibition of Pka and a Pkb Mimic.

Lauber, B.S., Hardegger, L.A., Asraful, A.K., Lund, B.A., Dumele, O., Harder, M., Kuhn, B., Engh, R.A., Diederich, F.

(2016) Chemistry 22: 211

  • DOI: 10.1002/chem.201503552
  • Primary Citation of Related Structures:  
    4UJ1, 4UJ2, 4UJ9, 4UJA, 4UJB, 4Z83, 4Z84

  • PubMed Abstract: 

    • Protein kinases continue to be hot targets in drug discovery research, as they are involved in many essential cellular processes and their deregulation can lead to a variety of diseases. A series of 32 enantiomerically pure inhibitors was synthesized and tested towards protein kinase A (PKA) and protein kinase B mimic PKAB3 (PKA triple mutant) ...

    Protein kinases continue to be hot targets in drug discovery research, as they are involved in many essential cellular processes and their deregulation can lead to a variety of diseases. A series of 32 enantiomerically pure inhibitors was synthesized and tested towards protein kinase A (PKA) and protein kinase B mimic PKAB3 (PKA triple mutant). The ligands bind to the hinge region, ribose pocket, and glycine-rich loop at the ATP site. Biological assays showed high potency against PKA, with Ki values in the low nanomolar range. The investigation demonstrates the significance of targeting the often neglected glycine-rich loop for gaining high binding potency. X-ray co-crystal structures revealed a multi-facetted network of ligand-loop interactions for the tightest binders, involving orthogonal dipolar contacts, sulfur and other dispersive contacts, amide-π stacking, and H-bonding to organofluorine, besides efficient water replacement. The network was analyzed in a computational approach.

    Organizational Affiliation: 

    Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland), Fax: (+41) 44-632-11-09. diederich@org.chem.ethz.ch.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHAA351Homo 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
GTEx:  ENSG00000072062
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDEB20Homo sapiensMutation(s): 0 
Gene Names: PKIA, PRKACN1
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
PHAROS:  P61925
GTEx:  ENSG00000171033
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4L7 (Subject of Investigation/LOI)
Query on 4L7
Download Ideal Coordinates CCD File 
C [auth A]7-{(3S,4R)-4-[(5-bromothiophen-2-yl)carbonyl]pyrrolidin-3-yl}quinazolin-4(3H)-one
C17 H14 Br N3 O2 S
ZYTJGVHIDBAIRI-NEPJUHHUSA-N		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
E [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
BR
Query on BR
Download Ideal Coordinates CCD File 
D [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO		AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.24α = 90
b = 74.92β = 90
c = 80.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  


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Entry History 

Deposition Data

  • Deposited Date: 2015-04-09 
  • Released Date: 2016-04-13 
    • Deposition Author(s): Alam, K.A., Engh, R.A.

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2019-02-06
    Changes: Data collection, Experimental preparation