5OK3

Crystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp241 and Fasudil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.588 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Diamondoid Amino Acid-Based Peptide Kinase A Inhibitor Analogues.

Muller, J.Kirschner, R.A.Berndt, J.P.Wulsdorf, T.Metz, A.Hrdina, R.Schreiner, P.R.Geyer, A.Klebe, G.

(2019) Chemmedchem 14: 663-672

  • DOI: 10.1002/cmdc.201800779

  • PubMed Abstract: 
  • The incorporation of diamondoid amino acids (DAAs) into peptide-like drugs is a general strategy to improve lipophilicity, membrane permeability, and metabolic stability of peptidomimetic pharmaceuticals. We designed and synthesized five novel peptid ...

    The incorporation of diamondoid amino acids (DAAs) into peptide-like drugs is a general strategy to improve lipophilicity, membrane permeability, and metabolic stability of peptidomimetic pharmaceuticals. We designed and synthesized five novel peptidic DAA-containing kinase inhibitors of protein kinase A using a sophisticated molecular dynamics protocol and solid-phase peptide synthesis. By means of a thermophoresis binding assay, NMR, and crystal structure analysis, we determined the influence of the DAAs on the secondary structure and binding affinity in comparison to the native protein kinase inhibitor, which is purely composed of proteinogenic amino acids. Affinity and binding pose are largely conserved. One variant showed 6.5-fold potency improvement, most likely related to its increased side chain lipophilicity. A second variant exhibited slightly decreased affinity presumably due to loss of hydrogen-bond contacts to surrounding water molecules of the first solvation shell.


    Organizational Affiliation

    Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea.,Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; baumeist@biochem.mpg.de.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea. sglee@kribb.re.kr.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA. I.vanRhijn@uu.nl.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands. I.vanRhijn@uu.nl.,Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.,Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea. sglee@kribb.re.kr.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.,Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.,Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032, Marburg, Germany.,Stratingh Institute for Chemistry, University of Groningen, 9747AG, Groningen, The Netherlands.,Department of Biophysics, Ruhr University Bochum, 44801 Bochum, Germany.,Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK. Jamie.rossjohn@monash.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
A
353Cricetulus griseusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
Find proteins for P25321 (Cricetulus griseus)
Go to Gene View: PRKACA
Go to UniProtKB:  P25321
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UPF0418 protein FAM164A
D
18Cricetulus griseusMutation(s): 1 
Find proteins for G3HK48 (Cricetulus griseus)
Go to UniProtKB:  G3HK48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M77
Query on M77

Download SDF File 
Download CCD File 
A
5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE
Fasudil, (5-ISOQUINOLINESULFONYL)HOMOPIPERAZINE
C14 H17 N3 O2 S
NGOGFTYYXHNFQH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 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
BW5
Query on BW5
D
L-peptide linkingC13 H21 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.588 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.609α = 90.00
b = 73.281β = 90.00
c = 108.428γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Loewe-CorporationGermany--

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-05-15
    Type: Data collection, Database references