5N3C | pdb_00005n3c

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

• PDB DOI: https://doi.org/10.2210/pdb5N3C/pdb

• Classification: TRANSFERASE
• Organism(s): Cricetulus griseus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-08 Released: 2018-02-28 
• Deposition Author(s): Siefker, C., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

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 

• PubMed: 33021032 
• DOI: https://doi.org/10.1002/anie.202011295
• Primary Citation 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.

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Organizational Affiliation: 
• Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany.
Roche Innovation Center, Grenzacherstr. 124, 4070, Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.43 kDa 
• Atom Count: 3,234 
• Modeled Residue Count: 365 
• Deposited Residue Count: 372 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	353	Cricetulus griseus	Mutation(s): 0  Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P25321 (Cricetulus griseus) Explore P25321  Go to UniProtKB:  P25321

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP dependent protein kinase inhibitor alpha-like protein	B	19	Cricetulus griseus	Mutation(s): 0
UniProt
Find proteins for G3HK48 (Cricetulus griseus) Explore G3HK48  Go to UniProtKB:  G3HK48

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8M2	C [auth A]	[azanyl(thiophen-3-yl)methylidene]azanium C5 H7 N2 S JKCKRNYECSTMLV-UHFFFAOYSA-O
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.513	α = 90
b = 72.728	β = 90
c = 108.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Siefker, C., Heine, A., Klebe, G.

Revision History  

• 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
• Version 1.4: 2024-10-09
  Changes: Structure summary