5O9Q

Crystal structure of ScGas2 in complex with compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Inhibitors against Fungal Cell Wall Remodeling Enzymes.

Delso, I.Valero-Gonzalez, J.Gomollon-Bel, F.Castro-Lopez, J.Fang, W.Navratilova, I.van Aalten, D.M.F.Tejero, T.Merino, P.Hurtado-Guerrero, R.

(2018) ChemMedChem 13: 128-132

  • DOI: https://doi.org/10.1002/cmdc.201700720
  • Primary Citation of Related Structures:  
    5O9O, 5O9P, 5O9Q, 5O9R, 5O9Y, 5OA2, 5OA6

  • PubMed Abstract: 

    Fungal β-1,3-glucan glucanosyltransferases are glucan-remodeling enzymes that play important roles in cell wall integrity, and are essential for the viability of pathogenic fungi and yeasts. As such, they are considered possible drug targets, although inhibitors of this class of enzymes have not yet been reported. Herein we report a multidisciplinary approach based on a structure-guided design using a highly conserved transglycosylase from Sacharomyces cerevisiae, that leads to carbohydrate derivatives with high affinity for Aspergillus fumigatus Gel4. We demonstrate by X-ray crystallography that the compounds bind in the active site of Gas2/Gel4 and interact with the catalytic machinery. The topological analysis of noncovalent interactions demonstrates that the combination of a triazole with positively charged aromatic moieties are important for optimal interactions with Gas2/Gel4 through unusual pyridinium cation-π and face-to-face π-π interactions. The lead compound is capable of inhibiting AfGel4 with an IC 50 value of 42 μm.


  • Organizational Affiliation

    Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009, Zaragoza, Aragón, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1,3-beta-glucanosyltransferase GAS2555Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GAS2YLR343WL8300.5
EC: 2.4.1
UniProt
Find proteins for Q06135 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06135 
Go to UniProtKB:  Q06135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06135
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose
B
3N/A
Glycosylation Resources
GlyTouCan:  G00024MO
GlyCosmos:  G00024MO
GlyGen:  G00024MO
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9PH
Query on 9PH

Download Ideal Coordinates CCD File 
C [auth A](2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-3,5-bis(oxidanyl)-6-[4-(phenylmethoxymethyl)-1,2,3-triazol-1-yl]oxan-4-yl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-oxane-3,4,5-triol
C28 H41 N3 O16
CUNJJKLJJLQYMH-ZJLPYKFYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.963α = 90
b = 70.508β = 90
c = 150.585γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary