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 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
A
351Homo sapiensMutation(s): 0 
Gene Names: PRKACA (PKACA)
EC: 2.7.11.11
Find proteins for P17612 (Homo sapiens)
Go to Gene View: PRKACA
Go to UniProtKB:  P17612
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE
B
20Homo sapiensMutation(s): 0 
Gene Names: PKIA (PRKACN1)
Find proteins for P61925 (Homo sapiens)
Go to Gene View: PKIA
Go to UniProtKB:  P61925
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR
Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
MPD
Query on MPD
Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
4L7
Query on 4L7
Download SDF File 
Download CCD File 
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
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.240α = 90.00
b = 74.920β = 90.00
c = 80.040γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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 

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