4BDT

Human acetylcholinesterase in complex with huprine W and fasciculin 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal structures of human cholinesterases in complex with huprine W and tacrine: elements of specificity for anti-Alzheimer's drugs targeting acetyl- and butyryl-cholinesterase.

Nachon, F.Carletti, E.Ronco, C.Trovaslet, M.Nicolet, Y.Jean, L.Renard, P.Y.

(2013) Biochem J 453: 393-399

  • DOI: 10.1042/BJ20130013
  • Primary Citation of Related Structures:  
    4BDS, 4BDT

  • PubMed Abstract: 
  • The multifunctional nature of Alzheimer's disease calls for MTDLs (multitarget-directed ligands) to act on different components of the pathology, like the cholinergic dysfunction and amyloid aggregation. Such MTDLs are usually on the basis of cholinesterase inhibitors (e ...

    The multifunctional nature of Alzheimer's disease calls for MTDLs (multitarget-directed ligands) to act on different components of the pathology, like the cholinergic dysfunction and amyloid aggregation. Such MTDLs are usually on the basis of cholinesterase inhibitors (e.g. tacrine or huprine) coupled with another active molecule aimed at a different target. To aid in the design of these MTDLs, we report the crystal structures of hAChE (human acetylcholinesterase) in complex with FAS-2 (fasciculin 2) and a hydroxylated derivative of huprine (huprine W), and of hBChE (human butyrylcholinesterase) in complex with tacrine. Huprine W in hAChE and tacrine in hBChE reside in strikingly similar positions highlighting the conservation of key interactions, namely, π-π/cation-π interactions with Trp86 (Trp82), and hydrogen bonding with the main chain carbonyl of the catalytic histidine residue. Huprine W forms additional interactions with hAChE, which explains its superior affinity: the isoquinoline moiety is associated with a group of aromatic residues (Tyr337, Phe338 and Phe295 not present in hBChE) in addition to Trp86; the hydroxyl group is hydrogen bonded to both the catalytic serine residue and residues in the oxyanion hole; and the chlorine substituent is nested in a hydrophobic pocket interacting strongly with Trp439. There is no pocket in hBChE that is able to accommodate the chlorine substituent.


    Organizational Affiliation

    Département de Toxicologie, Institut de Recherche Biomédicale des Armées, 24 Avenue des Maquis du Grésivaudan, BP87, 38702 La Tronche, France. florian@nachon.net



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYLCHOLINESTERASEA583Homo sapiensMutation(s): 0 
Gene Names: ACHE
EC: 3.1.1.7
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P22303 (Homo sapiens)
Explore P22303 
Go to UniProtKB:  P22303
PHAROS:  P22303
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FASCICULIN-2B61Dendroaspis angusticepsMutation(s): 0 
UniProt
Find proteins for P0C1Z0 (Dendroaspis angusticeps)
Explore P0C1Z0 
Go to UniProtKB:  P0C1Z0
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G28454KX
GlyCosmos:  G28454KX
GlyGen:  G28454KX
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HUW (Subject of Investigation/LOI)
Query on HUW

Download Ideal Coordinates CCD File 
D [auth A]HUPRINE W
C18 H19 Cl N2 O
GAOPELPOAHCRBF-NWDGAFQWSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
O [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HUW PDBBind:  4BDT IC50: 1.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.6α = 90
b = 151.6β = 90
c = 246.4γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references
  • Version 1.2: 2018-02-28
    Changes: Advisory, Database references, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary