6U77 | pdb_00006u77

yGsy2p in complex with small molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.259 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.202 (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 1.3 of the entry. See complete history

Literature

Discovery and Development of Small-Molecule Inhibitors of Glycogen Synthase.

Tang, B.Frasinyuk, M.S.Chikwana, V.M.Mahalingan, K.K.Morgan, C.A.Segvich, D.M.Bondarenko, S.P.Mrug, G.P.Wyrebek, P.Watt, D.S.DePaoli-Roach, A.A.Roach, P.J.Hurley, T.D.

(2020) J Med Chem 63: 3538-3551

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01851
  • Primary Citation Related Structures: 
    6U77

  • PubMed Abstract: 

    The overaccumulation of glycogen appears as a hallmark in various glycogen storage diseases (GSDs), including Pompe, Cori, Andersen, and Lafora disease. Accumulating evidence suggests that suppression of glycogen accumulation represents a potential therapeutic approach for treating these GSDs. Using a fluorescence polarization assay designed to screen for inhibitors of the key glycogen synthetic enzyme, glycogen synthase (GS), we identified a substituted imidazole, ( rac )-2-methoxy-4-(1-(2-(1-methylpyrrolidin-2-yl)ethyl)-4-phenyl-1 H -imidazol-5-yl)phenol ( H23 ), as a first-in-class inhibitor for yeast GS 2 (yGsy2p). Data from X-ray crystallography at 2.85 Å, as well as kinetic data, revealed that H23 bound within the uridine diphosphate glucose binding pocket of yGsy2p. The high conservation of residues between human and yeast GS in direct contact with H23 informed the development of around 500 H23 analogs. These analogs produced a structure-activity relationship profile that led to the identification of a substituted pyrazole, 4-(4-(4-hydroxyphenyl)-3-(trifluoromethyl)-1 H -pyrazol-5-yl)pyrogallol, with a 300-fold improved potency against human GS. These substituted pyrazoles possess a promising scaffold for drug development efforts targeting GS activity in GSDs associated with excess glycogen accumulation.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202, Indiana, United States.

Macromolecule Content 

  • Total Structure Weight: 323.23 kDa 
  • Atom Count: 20,692 
  • Modeled Residue Count: 2,546 
  • Deposited Residue Count: 2,820 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycogen [starch] synthase isoform 2
A, B, C, D
705Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GSY2YLR258WL8479.8
EC: 2.4.1.11
UniProt
Find proteins for P27472 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P27472 
Go to UniProtKB:  P27472
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27472
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VMC
(Subject of Investigation/LOI)

Query on VMC



Download:Ideal Coordinates CCD File
F [auth A],
J [auth C],
L [auth D]
2-methoxy-4-(1-{2-[(2S)-1-methylpyrrolidin-2-yl]ethyl}-4-phenyl-1H-imidazol-5-yl)phenol
C23 H27 N3 O2
YGPHAIXUDLLWHC-IBGZPJMESA-N
G6P

Query on G6P



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
H [auth B],
I [auth C],
K [auth D]
6-O-phosphono-alpha-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-DVKNGEFBSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.259 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.257α = 90
b = 206.557β = 90
c = 205.035γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01-DK079887

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary