7P1P

Crystal structure of human acetylcholinesterase in complex with (E)-3-hydroxy-6-(3-(4-(4-(((2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)butyl)-1H-1,2,3-triazol-1-yl)propyl)picolinaldehyde oxime


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

A New Class of Bi- and Trifunctional Sugar Oximes as Antidotes against Organophosphorus Poisoning.

Da Silva, O.Probst, N.Landry, C.Hanak, A.S.Warnault, P.Coisne, C.Calas, A.G.Gosselet, F.Courageux, C.Gastellier, A.J.Trancart, M.Baati, R.Dehouck, M.P.Jean, L.Nachon, F.Renard, P.Y.Dias, J.

(2022) J Med Chem 65: 4649-4666

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01748
  • Primary Citation of Related Structures:  
    7P1N, 7P1P

  • PubMed Abstract: 

    Recent events demonstrated that organophosphorus nerve agents are a serious threat for civilian and military populations. The current therapy includes a pyridinium aldoxime reactivator to restore the enzymatic activity of acetylcholinesterase located in the central nervous system and neuro-muscular junctions. One major drawback of these charged acetylcholinesterase reactivators is their poor ability to cross the blood-brain barrier. In this study, we propose to evaluate glucoconjugated oximes devoid of permanent charge as potential central nervous system reactivators. We determined their in vitro reactivation efficacy on inhibited human acetylcholinesterase, the crystal structure of two compounds in complex with the enzyme, their protective index on intoxicated mice, and their pharmacokinetics. We then evaluated their endothelial permeability coefficients with a human in vitro model. This study shed light on the structural restrains of new sugar oximes designed to reach the central nervous system through the glucose transporter located at the blood-brain barrier.


  • Organizational Affiliation

    Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale Des Armées, F-91220 Brétigny-Sur-Orge, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AcetylcholinesteraseA [auth aa],
C [auth bb]
257Homo sapiensMutation(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
GTEx:  ENSG00000087085 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22303
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AcetylcholinesteraseB [auth A],
D [auth B]
282Homo sapiensMutation(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
GTEx:  ENSG00000087085 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22303
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E]3N/A
Glycosylation Resources
GlyTouCan:  G00065MO
GlyCosmos:  G00065MO
GlyGen:  G00065MO
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4IX (Subject of Investigation/LOI)
Query on 4IX

Download Ideal Coordinates CCD File 
H [auth aa](2R,3R,4S,5S,6R)-2-[4-[1-[3-[6-[(Z)-hydroxyiminomethyl]-5-oxidanyl-pyridin-2-yl]propyl]-1,2,3-triazol-4-yl]butoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
C21 H31 N5 O8
XSKZXNAZWMWYGQ-WXHIOXNPSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth bb]
CA [auth bb]
HA [auth B]
I [auth aa]
IA [auth B]
BA [auth bb],
CA [auth bb],
HA [auth B],
I [auth aa],
IA [auth B],
J [auth aa],
JA [auth B],
K [auth aa],
KA [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth A]
EA [auth bb]
FA [auth bb]
GA [auth bb]
L [auth aa]
AA [auth A],
EA [auth bb],
FA [auth bb],
GA [auth bb],
L [auth aa],
M [auth aa],
N [auth aa],
NA [auth B],
OA [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
X [auth A],
Y [auth A],
Z [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth bb],
LA [auth B],
MA [auth B],
U [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.863α = 90
b = 211.863β = 90
c = 116.269γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2022-03-16
    Changes: Database references
  • Version 1.3: 2022-04-06
    Changes: Database references
  • Version 1.4: 2022-06-08
    Changes: Database references
  • Version 1.5: 2024-01-31
    Changes: Data collection, Refinement description