8RVK

Maltodextrin phosphorylase (MalP) in complex with a alpha-1,2-cyclophellitol analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Conformational and Electronic Variations in 1,2- and 1,5a-Cyclophellitols and their Impact on Retaining alpha-Glucosidase Inhibition.

Ofman, T.P.Heming, J.J.A.Nin-Hill, A.Kullmer, F.Moran, E.Bennett, M.Steneker, R.Klein, A.M.Ruijgrok, G.Kok, K.Armstrong, Z.W.B.Aerts, J.M.F.G.van der Marel, G.A.Rovira, C.Davies, G.J.Artola, M.Codee, J.D.C.Overkleeft, H.S.

(2024) Chemistry 30: e202400723-e202400723

  • DOI: https://doi.org/10.1002/chem.202400723
  • Primary Citation of Related Structures:  
    8RVK, 8RW3

  • PubMed Abstract: 

    Glycoside hydrolases (glycosidases) take part in myriad biological processes and are important therapeutic targets. Competitive and mechanism-based inhibitors are useful tools to dissect their biological role and comprise a good starting point for drug discovery. The natural product, cyclophellitol, a mechanism-based, covalent and irreversible retaining β-glucosidase inhibitor has inspired the design of diverse α- and β-glycosidase inhibitor and activity-based probe scaffolds. Here, we sought to deepen our understanding of the structural and functional requirements of cyclophellitol-type compounds for effective human α-glucosidase inhibition. We synthesized a comprehensive set of α-configured 1,2- and 1,5a-cyclophellitol analogues bearing a variety of electrophilic traps. The inhibitory potency of these compounds was assessed towards both lysosomal and ER retaining α-glucosidases. These studies revealed the 1,5a-cyclophellitols to be the most potent retaining α-glucosidase inhibitors, with the nature of the electrophile determining inhibitory mode of action (covalent or non-covalent). DFT calculations support the ability of the 1,5a-cyclophellitols, but not the 1,2-congeners, to adopt conformations that mimic either the Michaelis complex or transition state of α-glucosidases.


  • Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin phosphorylase
A, B
797Escherichia coli K-12Mutation(s): 0 
Gene Names: malPb3417JW5689
EC: 2.4.1.1
UniProt
Find proteins for P00490 (Escherichia coli (strain K12))
Explore P00490 
Go to UniProtKB:  P00490
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00490
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H3V (Subject of Investigation/LOI)
Query on A1H3V

Download Ideal Coordinates CCD File 
C [auth A](3~{a}~{R},4~{R},5~{R},6~{R},7~{a}~{S})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3~{a},4,5,6,7,7~{a}-hexahydro-3~{H}-1,3-benzoxazol-2-one
C8 H13 N O5
MSEYXKZOSYTDQB-VOQCIKJUSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CA [auth B]
F [auth A]
H [auth A]
T [auth A]
UA [auth B]
CA [auth B],
F [auth A],
H [auth A],
T [auth A],
UA [auth B],
VA [auth B],
WA [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
BA [auth A]
BB [auth B]
CB [auth B]
AA [auth A],
AB [auth B],
BA [auth A],
BB [auth B],
CB [auth B],
DB [auth B],
EB [auth B],
FB [auth B],
GB [auth B],
HB [auth B],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
XA [auth B],
Y [auth A],
YA [auth B],
Z [auth A],
ZA [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
DA [auth B]
E [auth A]
EA [auth B]
FA [auth B]
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
FA [auth B],
G [auth A],
GA [auth B],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
TA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.498α = 90
b = 119.79β = 90
c = 150.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata scaling
Cootmodel building
MOLREPphasing
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union951231

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references