7K9O

Co-crystal structure of alpha glucosidase with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

N-Substituted Valiolamine Derivatives as Potent Inhibitors of Endoplasmic Reticulum alpha-Glucosidases I and II with Antiviral Activity.

Karade, S.S.Hill, M.L.Kiappes, J.L.Manne, R.Aakula, B.Zitzmann, N.Warfield, K.L.Treston, A.M.Mariuzza, R.A.

(2021) J Med Chem 64: 18010-18024

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01377
  • Primary Citation of Related Structures:  
    7JTY, 7K9N, 7K9O, 7K9Q, 7K9T, 7KAD, 7KB6, 7KB8, 7KBJ, 7KBR, 7KRY, 7L9E

  • PubMed Abstract: 

    Most enveloped viruses rely on the host cell endoplasmic reticulum (ER) quality control (QC) machinery for proper folding of glycoproteins. The key ER α-glucosidases (α-Glu) I and II of the ERQC machinery are attractive targets for developing broad-spectrum antivirals. Iminosugars based on deoxynojirimycin have been extensively studied as ER α-glucosidase inhibitors; however, other glycomimetic compounds are less established. Accordingly, we synthesized a series of N-substituted derivatives of valiolamine, the iminosugar scaffold of type 2 diabetes drug voglibose. To understand the basis for up to 100,000-fold improved inhibitory potency, we determined high-resolution crystal structures of mouse ER α-GluII in complex with valiolamine and 10 derivatives. The structures revealed extensive interactions with all four α-GluII subsites. We further showed that N-substituted valiolamines were active against dengue virus and SARS-CoV-2 in vitro . This study introduces valiolamine-based inhibitors of the ERQC machinery as candidates for developing potential broad-spectrum therapeutics against the existing and emerging viruses.


  • Organizational Affiliation

    University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha glucosidase 2 alpha neutral subunit
A, C
977Mus musculusMutation(s): 1 
Gene Names: Ganab
UniProt
Find proteins for A1A4T2 (Mus musculus)
Explore A1A4T2 
Go to UniProtKB:  A1A4T2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1A4T2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosidase 2 subunit beta
B, D
547Mus musculusMutation(s): 0 
Gene Names: Prkcsh
UniProt & NIH Common Fund Data Resources
Find proteins for O08795 (Mus musculus)
Explore O08795 
Go to UniProtKB:  O08795
IMPC:  MGI:107877
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08795
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W9P (Subject of Investigation/LOI)
Query on W9P

Download Ideal Coordinates CCD File 
BA [auth C],
E [auth A]
(1~{S},2~{S},3~{R},4~{S},5~{S})-1-(hydroxymethyl)-5-[6-[[2-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-4-(1,2,3,4-tetrazol-1-yl)phenyl]amino]hexylamino]cyclohexane-1,2,3,4-tetrol
C20 H31 N7 O7
AEVYKERIFGNKMO-UVBQOVKKSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
IA [auth C],
J [auth A],
K [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
DA [auth C],
M [auth A],
R [auth A],
X [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
EA [auth C]
F [auth A]
FA [auth C]
G [auth A]
AA [auth B],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
JA [auth C],
KA [auth C],
L [auth A],
LA [auth C],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
PA [auth C],
Q [auth A],
QA [auth C],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
RA [auth D],
SA [auth D],
Y [auth B],
Z [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.716α = 90
b = 102.716β = 90
c = 239.625γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2022-01-05
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description