5FKY

Structure of a hydrolase bound with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Analysis of transition state mimicry by tight binding aminothiazoline inhibitors provides insight into catalysis by humanO-GlcNAcase.

Cekic, N.Heinonen, J.E.Stubbs, K.A.Roth, C.He, Y.Bennet, A.J.McEachern, E.J.Davies, G.J.Vocadlo, D.J.

(2016) Chem Sci 7: 3742-3750

  • DOI: 10.1039/c6sc00370b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The modification of nucleocytoplasmic proteins with <i>O </i>-linked <i>N </i>-acetylglucosamine ( <i>O </i>-GlcNAc) plays diverse roles in multicellular organisms. Inhibitors of <i>O </i>-GlcNAc hydrolase (OGA), the enzyme that removes <i>O </i> ...

    The modification of nucleocytoplasmic proteins with O -linked N -acetylglucosamine ( O -GlcNAc) plays diverse roles in multicellular organisms. Inhibitors of O -GlcNAc hydrolase (OGA), the enzyme that removes O -GlcNAc from proteins, lead to increased O -GlcNAc levels in cells and are seeing widespread adoption in the field as a research tool used in cells and in vivo . Here we synthesize and study a series of tight binding carbohydrate-based inhibitors of human OGA (hOGA). The most potent of these 2'-aminothiazolines binds with a sub-nanomolar K i value to hOGA (510 ± 50 pM) and the most selective has greater than 1 800 000-fold selectivity for hOGA over mechanistically related human lysosomal β-hexosaminidase. Structural data of inhibitors in complex with an hOGA homologue reveals the basis for variation in binding among these compounds. Using linear free energy analyses, we show binding of these 2'-aminothiazoline inhibitors depends on the p K a of the aminothiazoline ring system, revealing the protonation state of the inhibitor is a key driver of binding. Using series of inhibitors and synthetic substrates, we show that 2'-aminothiazoline inhibitors are transition state analogues of hOGA that bind to the enzyme up to 1-million fold more tightly than the substrate. These collective data support an oxazoline, rather than a protonated oxazolinium ion, intermediate being formed along the reaction pathway. Inhibitors from this series will prove generally useful tools for the study of O -GlcNAc. The new insights gained here, into the catalytic mechanism of hOGA and the fundamental drivers of potency and selectivity of OGA inhibitors, should enable tuning of hOGA inhibitors with desirable properties.


    Organizational Affiliation

    Sprint Bioscience , 141 57 Huddinge , Sweden.,School of Chemistry and Biochemistry , The University of Western Australia (M313) , 35 Stirling Highway , Crawley , WA 6009 , Australia.,Department of Food Science, National (Taiwan) Ocean University, Keelung, 202, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.,Polgenix Inc., Cleveland, OH 44106, USA.,Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045.,Research Center for Materials Science, Nagoya University, Nagoya, Japan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.,Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045.,Discovery Sciences, IMED Biotech Unit , AstraZeneca , S-43183 Mölndal , Sweden.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Kyoto Sangyo University, Kyoto, Japan.,Discovery Safety, Drug Safety and Metabolism, IMED Biotech Unit , AstraZeneca , Waltham , Massachusetts 02451 , United States.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.,York Structural Biology Laboratory , Department of Chemistry , The University of York , YO10 5DD , UK.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan tendo@cc.kyoto-su.ac.jp.,Charnwood Molecular , Loughborough LE11 5DA , U.K.,Neuroscience, IMED Biotech Unit , AstraZeneca , Cambridge CB21 6GH , U.K.,University of Puerto Rico at Humacao, Humacao, PR, USA.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Nagoya University, Nagoya, Japan.,Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan.,Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506.,Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , 141 57 Huddinge , Sweden.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047.,Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan.,IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois, 60439.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada . Email: dvocadlo@sfu.ca.,Oncology Chemistry, IMED Biotech Unit , AstraZeneca , Cambridge CB4 0WG , U.K.,Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: murafuji.hidenobu.bj@daiichisankyo.co.jp.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: muto.tsuyoshi.zu@daiichisankyo.co.jp.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.,Department of Biochemistry, National Centre of Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.,Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-GLCNACASE BT_4395
A, B
716Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
EC: 3.2.1.169
Find proteins for Q89ZI2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q89ZI2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2J4
Query on 2J4

Download SDF File 
Download CCD File 
A, B
(3aR,5R,6S,7R,7aR)-2-amino-5-(hydroxymethyl)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol
C7 H12 N2 O4 S
PUFNZEXJKQHIQN-QZABAPFNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.211 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.440α = 104.07
b = 93.690β = 94.18
c = 99.020γ = 102.97
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2017-02-01
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other
  • Version 1.2: 2018-08-29
    Type: Data collection, Database references