Crystal structure of a bacterial fucosidase with inhibitor FucPUG

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Synthetic and Crystallographic Insight into Exploiting sp2Hybridization in the Development of alpha-l-Fucosidase Inhibitors.

Coyle, T.Wu, L.Debowski, A.W.Davies, G.J.Stubbs, K.A.

(2019) Chembiochem 20: 1365-1368

  • DOI: https://doi.org/10.1002/cbic.201800710
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The sugar fucose plays a myriad of roles in biological recognition. Enzymes hydrolyzing fucose from glycoconjugates, α-l-fucosidases, are important targets for inhibitor and probe development. Here we describe the synthesis and evaluation of novel α-l-fucosidase inhibitors, with X-ray crystallographic analysis using an α-l-fucosidase from Bacteroides thetaiotamicron helping to lay a foundation for future development of inhibitors for this important enzyme class.

  • Organizational Affiliation

    School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
475Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_2970
Find proteins for Q8A3I4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A3I4 
Go to UniProtKB:  Q8A3I4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A3I4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GYZ (Subject of Investigation/LOI)
Query on GYZ

Download Ideal Coordinates CCD File 
N [auth A],
Y [auth B]
[(~{Z})-[(3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-ylidene]amino] ~{N}-phenylcarbamate
C13 H16 N2 O6
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
O [auth A]
P [auth A]
Q [auth A]
AA [auth B],
BA [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
Z [auth B]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
GYZ Binding MOAD:  6HZY Ki: 1.21e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.925α = 90
b = 84.602β = 109
c = 121.737γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Australian Research CouncilAustraliaFT100100291
National Health and Medical Research Council (Australia)AustraliaAPP1073250
European Research CouncilUnited KingdomERC-2012-AdG-322942

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description