5O9P | pdb_00005o9p

Crystal structure of Gas2 in complex with compound 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 63.16 kDa 
  • Atom Count: 3,823 
  • Modeled Residue Count: 435 
  • Deposited Residue Count: 555 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9P8

Query on 9P8



Download:Ideal Coordinates CCD File
B [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-(pyridin-2-ylmethoxymethyl)-1,2,3-triazol-1-yl]oxan-4-yl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-oxane-3,4,5-triol
C27 H40 N4 O16
GZCRLDXRIWVPBY-FLQYNTDFSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.067α = 90
b = 70.953β = 90
c = 150.99γ = 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 1.1: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary