5N6S

Thermotoga maritima family 1 Glycoside hydrolase complexed with Carba-Cyclophellitol transition state mimic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Carba-cyclophellitols Are Neutral Retaining-Glucosidase Inhibitors.

Beenakker, T.J.M.Wander, D.P.A.Offen, W.A.Artola, M.Raich, L.Ferraz, M.J.Li, K.Y.Houben, J.H.P.M.van Rijssel, E.R.Hansen, T.van der Marel, G.A.Codee, J.D.C.Aerts, J.M.F.G.Rovira, C.Davies, G.J.Overkleeft, H.S.

(2017) J. Am. Chem. Soc. 139: 6534-6537

  • DOI: 10.1021/jacs.7b01773
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The conformational analysis of glycosidases affords a route to their specific inhibition through transition-state mimicry. Inspired by the rapid reaction rates of cyclophellitol and cyclophellitol aziridine-both covalent retaining β-glucosidase inhib ...

    The conformational analysis of glycosidases affords a route to their specific inhibition through transition-state mimicry. Inspired by the rapid reaction rates of cyclophellitol and cyclophellitol aziridine-both covalent retaining β-glucosidase inhibitors-we postulated that the corresponding carba "cyclopropyl" analogue would be a potent retaining β-glucosidase inhibitor for those enzymes reacting through the 4H3 transition-state conformation. Ab initio metadynamics simulations of the conformational free energy landscape for the cyclopropyl inhibitors show a strong bias for the 4H3 conformation, and carba-cyclophellitol, with an N-(4-azidobutyl)carboxamide moiety, proved to be a potent inhibitor (Ki = 8.2 nM) of the Thermotoga maritima TmGH1 β-glucosidase. 3-D structural analysis and comparison with unreacted epoxides show that this compound indeed binds in the 4H3 conformation, suggesting that conformational strain induced through a cyclopropyl unit may add to the armory of tight-binding inhibitor designs.


    Organizational Affiliation

    Department of Chemistry, University of York , Heslington, York, YO10 5DD, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-glucosidase A
A, B, C, D
468Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: bglA
EC: 3.2.1.21
Find proteins for Q08638 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q08638
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
8P5
Query on 8P5

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A, B, C, D
azanylidene-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)-7-bicyclo[4.1.0]heptanyl]carbonylamino]butylimino]azanium
C13 H23 N4 O5
AGQBRQFVJQUDGP-MQOZHFKUSA-O
 Ligand Interaction
IMD
Query on IMD

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A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
PEG
Query on PEG

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A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.239 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 71.626α = 72.34
b = 76.674β = 86.39
c = 95.257γ = 85.54
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-02-16 
  • Released Date: 2017-03-01 
  • Deposition Author(s): Offen, W., Davies, G.

Funding OrganizationLocationGrant Number
ERCUnited KingdomERC-2012-AdG-322942

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-05-10
    Type: Database references
  • Version 1.2: 2017-05-17
    Type: Database references
  • Version 1.3: 2017-05-24
    Type: Database references