6QAC

Human Butyrylcholinesterase in complex with (S)-2-(butylamino)-N-(3-cycloheptylpropyl)-3-(1H-indol-3-yl)propanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Tryptophan-derived butyrylcholinesterase inhibitors as promising leads against Alzheimer's disease.

Meden, A.Knez, D.Jukic, M.Brazzolotto, X.Grsic, M.Pislar, A.Zahirovic, A.Kos, J.Nachon, F.Svete, J.Gobec, S.Groselj, U.

(2019) Chem Commun (Camb) 55: 3765-3768

  • DOI: 10.1039/c9cc01330j
  • Primary Citation of Related Structures:  
    6QAA, 6QAC, 6QAB, 6QAE, 6QAD

  • PubMed Abstract: 
  • We have identified tryptophan-based selective nanomolar butyrylcholinesterase (BChE) inhibitors. They are defined according to their chemical modularity, novel binding mode revealed by five solved crystal structures with human BChE, low cytotoxicity, and predicted permeability of the blood-brain barrier ...

    We have identified tryptophan-based selective nanomolar butyrylcholinesterase (BChE) inhibitors. They are defined according to their chemical modularity, novel binding mode revealed by five solved crystal structures with human BChE, low cytotoxicity, and predicted permeability of the blood-brain barrier. Altogether, these factors indicate their potential as unique lead compounds for symptomatic therapy against Alzheimer's disease.


    Organizational Affiliation

    Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia. uros.groselj@fkkt.uni-lj.si.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CholinesteraseA557Homo sapiensMutation(s): 4 
Gene Names: BCHECHE1
EC: 3.1.1.8
Find proteins for P06276 (Homo sapiens)
Explore P06276 
Go to UniProtKB:  P06276
NIH Common Fund Data Resources
PHAROS:  P06276
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HUT
Query on HUT

Download Ideal Coordinates CCD File 
H [auth A](2~{S})-2-(butylamino)-~{N}-(3-cycloheptylpropyl)-3-(1~{H}-indol-3-yl)propanamide
C25 H39 N3 O
UWVIHWQBZNJHCM-DEOSSOPVSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], L [auth A], M [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
I [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.113α = 90
b = 154.113β = 90
c = 127.619γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Ministry of Armed ForcesFrancePDH-2-NRBC-3-C-3201

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary