7KAD | pdb_00007kad

Co-crystal structure of alpha glucosidase with compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.203 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.172 (Depositor) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 352.82 kDa 
  • Atom Count: 15,939 
  • Modeled Residue Count: 1,885 
  • Deposited Residue Count: 3,062 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Neutral alpha-glucosidase AB
A, C
977Mus musculusMutation(s): 1 
Gene Names: GanabG2anKiaa0088
EC: 3.2.1.207
UniProt
Find proteins for Q8BHN3 (Mus musculus)
Explore Q8BHN3 
Go to UniProtKB:  Q8BHN3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BHN3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glucosidase 2 subunit beta
B, D
554Mus 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
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W9Y
(Subject of Investigation/LOI)

Query on W9Y



Download:Ideal Coordinates CCD File
E [auth A],
UA [auth C]
(1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(1H-1,2,3-triazol-1-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol
C21 H32 N6 O7
XQDBSGWKEMRNGZ-RQUKQETFSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
NB [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
DA [auth A]
H [auth A]
I [auth A]
K [auth A]
T [auth A]
DA [auth A],
H [auth A],
I [auth A],
K [auth A],
T [auth A],
ZA [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth C]
BA [auth A]
CA [auth A]
DB [auth C]
AA [auth A],
AB [auth C],
BA [auth A],
CA [auth A],
DB [auth C],
FA [auth A],
IB [auth C],
KB [auth C],
M [auth A],
MB [auth C],
R [auth A],
U [auth A],
W [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
KA [auth A]
LA [auth A]
MA [auth A]
NA [auth A]
OA [auth A]
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
OB [auth C],
PB [auth C],
QB [auth C],
RB [auth C],
SB [auth C],
TB [auth C],
UB [auth C],
VB [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
BB [auth C]
CB [auth C]
EA [auth A]
EB [auth C]
F [auth A]
BB [auth C],
CB [auth C],
EA [auth A],
EB [auth C],
F [auth A],
FB [auth C],
G [auth A],
GA [auth A],
GB [auth C],
HA [auth A],
HB [auth C],
IA [auth A],
J [auth A],
JA [auth A],
JB [auth C],
L [auth A],
LB [auth C],
N [auth A],
O [auth A],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
RA [auth B],
S [auth A],
V [auth A],
VA [auth C],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
SA [auth B],
TA [auth B],
WB [auth D],
XB [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.203 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.172 (Depositor) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.689α = 90
b = 102.689β = 90
c = 240.275γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    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
  • Version 1.4: 2024-10-23
    Changes: Structure summary