Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 123.62 kDa 
• Atom Count: 8,353 
• Modelled Residue Count: 1,054 
• Deposited Residue Count: 1,106 
• Unique protein chains: 1

 7D9P

Crystal Structure of Recombinant Human Acetylcholinesterase in Complex with Compound 12

• PDB DOI:  https://doi.org/10.2210/pdb7D9P/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-10-14 Released: 2021-08-25 
• Deposition Author(s): Liu, Q.F., Yin, W.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Kinetics-Driven Drug Design Strategy for Next-Generation Acetylcholinesterase Inhibitors to Clinical Candidate.

Zhou, Y., Fu, Y., Yin, W., Li, J., Wang, W., Bai, F., Xu, S., Gong, Q., Peng, T., Hong, Y., Zhang, D., Zhang, D., Liu, Q., Xu, Y., Xu, H.E., Zhang, H., Jiang, H., Liu, H.

(2021) J Med Chem 64: 1844-1855

• PubMed: 33570950 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c01863
• Primary Citation of Related Structures:  
  7D9O, 7D9P, 7D9Q


• PubMed Abstract: 
  

The acetylcholinesterase (AChE) inhibitors remain key therapeutic drugs for the treatment of Alzheimer's disease (AD). However, the low-safety window limits their maximum therapeutic benefits. Here, a novel kinetics-driven drug design strategy was employed to discover new-generation AChE inhibitors that possess a longer drug-target residence time and exhibit a larger safety window. After detailed investigations, compound 12 was identified as a highly potent, highly selective, orally bioavailable, and brain preferentially distributed AChE inhibitor. Moreover, it significantly ameliorated cognitive impairments in different mouse models with a lower effective dose than donepezil. The X-ray structure of the cocrystal complex provided a precise binding mode between 12 and AChE. Besides, the data from the phase I trials demonstrated that 12 had good safety, tolerance, and pharmacokinetic profiles at all preset doses in healthy volunteers, providing a solid basis for its further investigation in phase II trials for the treatment of AD.

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Organizational Affiliation: 

School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A, B	553	Homo sapiens	Mutation(s): 0  Gene Names: ACHE EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P22303 (Homo sapiens) Explore P22303  Go to UniProtKB:  P22303
PHAROS:  P22303

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H0R (Subject of Investigation/LOI)	E [auth A], F [auth B]	(2S)-2-[[4-fluoranyl-1-[(2-fluorophenyl)methyl]piperidin-4-yl]methyl]-5,6-dimethoxy-2,3-dihydroinden-1-one C24 H27 F2 N O3 DCZOKUPYRTZAFN-SFHVURJKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.944	α = 90
b = 104.944	β = 90
c = 323.616	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-25 
Deposition Author(s): Liu, Q.F., Yin, W.C.

Revision History  

• Version 1.0: 2021-08-25
  Type: Initial release