6QA6

Glycogen Phosphorylase b in complex with 30

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 

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Literature

Glucopyranosylidene-spiro-imidazolinones, a New Ring System: Synthesis and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetics and X-ray Crystallography.

Szabo, K.E., Kyriakis, E., Psarra, A.G., Karra, A.G., Sipos, A., Docsa, T., Stravodimos, G.A., Katsidou, E., Skamnaki, V.T., Liggri, P.G.V., Zographos, S.E., Mandi, A., Kiraly, S.B., Kurtan, T., Leonidas, D.D., Somsak, L.

(2019) J Med Chem 62: 6116-6136

  • DOI: 10.1021/acs.jmedchem.9b00356
  • Primary Citation of Related Structures:  
    6QA6, 6QA7, 6QA8

  • PubMed Abstract: 

    • Epimeric series of aryl-substituted glucopyranosylidene-spiro-imidazolinones, an unprecedented new ring system, were synthesized from the corresponding Schiff bases of O -perbenzoylated (gluculopyranosylamine)onamides by intramolecular ring closure of the aldimine moieties with the carboxamide group elicited by N -bromosuccinimide in pyridine ...

    Epimeric series of aryl-substituted glucopyranosylidene-spiro-imidazolinones, an unprecedented new ring system, were synthesized from the corresponding Schiff bases of O -perbenzoylated (gluculopyranosylamine)onamides by intramolecular ring closure of the aldimine moieties with the carboxamide group elicited by N -bromosuccinimide in pyridine. Test compounds were obtained by Zemplén O -debenzoylation. Stereochemistry and ring tautomers of the new compounds were investigated by NMR, time-dependent density functional theory (TDDFT)-electronic circular dichroism, and DFT-NMR methods. Kinetic studies with rabbit muscle and human liver glycogen phosphorylases showed that the ( R )-imidazolinones were 14-216 times more potent than the ( S ) epimers. The 2-naphthyl-substituted ( R )-imidazolinone was the best inhibitor of the human enzyme ( K i 1.7 μM) and also acted on HepG2 cells (IC 50 177 μM). X-ray crystallography revealed that only the ( R ) epimers bound in the crystal. Their inhibitory efficacy is based on the hydrogen-bonding interactions of the carbonyl oxygen and the NH of the imidazolinone ring.

    Organizational Affiliation: 

    Department of Organic Chemistry , University of Debrecen , P.O. Box 400, H-4002 Debrecen , Hungary.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle formA843Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HT8
Query on HT8
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		(5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-2-naphthalen-2-yl-8,9,10-tris(oxidanyl)-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one
C18 H18 N2 O6
QSYAFZZRALZDHF-NSIVTLKISA-N		 Ligand Interaction
PLP
Query on PLP
Download Ideal Coordinates CCD File 
E [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
B [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HT8 Binding MOAD:  6QA6 Ki: 2110 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.161α = 90
b = 128.161β = 90
c = 115.794γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references