5N3C

cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule Thiophene-3-Carboximidamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts.

Oebbeke, M.Siefker, C.Wagner, B.Heine, A.Klebe, G.

(2020) Angew Chem Int Ed Engl 

  • DOI: https://doi.org/10.1002/anie.202011295
  • Primary Citation of Related Structures:  
    5N33, 5N3C, 5N3D, 5N3E, 5N3H, 5N3J, 5N3Q, 5N3S, 6SNN, 6SNX, 6SOX, 6SPM, 6SPS, 6SPU, 6SPY, 6YPS, 6Z08, 6Z44, 6ZN0

  • PubMed Abstract: 

    Medicinal-chemistry optimization follows strategies replacing functional groups and attaching larger substituents at a promising lead scaffold. Well-established bioisosterism rules are considered, however, it is difficult to estimate whether the introduced modifications really match the required properties at a binding site. The electron density distribution and pK a values are modulated influencing protonation states and bioavailability. Considering the adjacent H-bond donor/acceptor pattern of the hinge binding motif in a kinase, we studied by crystallography a set of fragments to map the required interaction pattern. Unexpectedly, benzoic acid and benzamidine, decorated with the correct substituents, are totally bioisosteric just as carboxamide and phenolic OH. A mono-dentate pyridine nitrogen out-performs bi-dentate functionalities. The importance of correctly designing pK a values of attached functional groups by additional substituents at the parent scaffold is rendered prominent.


  • Organizational Affiliation

    Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alpha353Cricetulus griseusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
UniProt
Find proteins for P25321 (Cricetulus griseus)
Explore P25321 
Go to UniProtKB:  P25321
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25321
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP dependent protein kinase inhibitor alpha-like protein19Cricetulus griseusMutation(s): 0 
UniProt
Find proteins for G3HK48 (Cricetulus griseus)
Explore G3HK48 
Go to UniProtKB:  G3HK48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3HK48
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8M2
Query on 8M2

Download Ideal Coordinates CCD File 
C [auth A][azanyl(thiophen-3-yl)methylidene]azanium
C5 H7 N2 S
JKCKRNYECSTMLV-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D 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: 1.77 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.513α = 90
b = 72.728β = 90
c = 108.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection
  • Version 1.2: 2020-12-09
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description