7AMD | pdb_00007amd

In situ assembly of choline acetyltransferase ligands by a hydrothiolation reaction reveals key determinants for inhibitor design

• PDB DOI: https://doi.org/10.2210/pdb7AMD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-10-08 Released: 2020-10-28 
• Deposition Author(s): Allgardsson, A., Ekstrom, F.J., Wiktelius, D., Bergstrom, T., Hoster, N., Akfur, C., Forsgren, N., Lejon, C., Hedenstrom, M., Linusson, A.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

In Situ Assembly of Choline Acetyltransferase Ligands by a Hydrothiolation Reaction Reveals Key Determinants for Inhibitor Design.

Wiktelius, D., Allgardsson, A., Bergstrom, T., Hoster, N., Akfur, C., Forsgren, N., Lejon, C., Hedenstrom, M., Linusson, A., Ekstrom, F.

(2021) Angew Chem Int Ed Engl 60: 813-819

• PubMed: 33079431 
• DOI: https://doi.org/10.1002/anie.202011989
• Primary Citation Related Structures: 
  7AMD


• PubMed Abstract: 
  

  The potential drug target choline acetyltransferase (ChAT) catalyses the production of the neurotransmitter acetylcholine in cholinergic neurons, T-cells, and B-cells. Herein, we show that arylvinylpyridiniums (AVPs), the most widely studied class of ChAT inhibitors, act as substrate in an unusual coenzyme A-dependent hydrothiolation reaction. This in situ synthesis yields an adduct that is the actual enzyme inhibitor. The adduct is deeply buried in the active site tunnel of ChAT and interactions with a hydrophobic pocket near the choline binding site have major implications for the molecular recognition of inhibitors. Our findings clarify the inhibition mechanism of AVPs, establish a drug modality that exploits a target-catalysed reaction between exogenous and endogenous precursors, and provide new directions for the development of ChAT inhibitors with improved potency and bioactivity.

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Organizational Affiliation: 
• Swedish Defence Research Agency, CBRN Defence and Security, 90187, Umeå, Sweden.
Department of Chemistry, Umeå University, 901 87, Umeå, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.17 kDa 
• Atom Count: 4,705 
• Modeled Residue Count: 575 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline O-acetyltransferase	A	612	Homo sapiens	Mutation(s): 7  Gene Names: CHAT EC: 2.3.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P28329 (Homo sapiens) Explore P28329  Go to UniProtKB:  P28329
PHAROS:  P28329 GTEx:  ENSG00000070748

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RMW (Subject of Investigation/LOI)	B [auth A]	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-2,2-dimethyl-4-[[3-[2-[(1~{R})-2-(1-methylpyridin-4-yl)-1-naphthalen-1-yl-ethyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate C39 H52 N8 O16 P3 S OYNQMIGIWWZLSR-UAMJECFJSA-O
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.614	α = 90
b = 71.836	β = 90
c = 169.597	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): Allgardsson, A., Ekstrom, F.J., Wiktelius, D., Bergstrom, T., Hoster, N., Akfur, C., Forsgren, N., Lejon, C., Hedenstrom, M., Linusson, A.

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Funding Organization	Location	Grant Number
Other government	Sweden	--

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2021-03-03
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description