6MA1

Crystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (11-26) and inhibitor 4a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors.

Martin, S.E.S.Tan, Z.W.Itkonen, H.M.Duveau, D.Y.Paulo, J.A.Janetzko, J.Boutz, P.L.Tork, L.Moss, F.A.Thomas, C.J.Gygi, S.P.Lazarus, M.B.Walker, S.

(2018) J Am Chem Soc 140: 13542-13545

  • DOI: https://doi.org/10.1021/jacs.8b07328
  • Primary Citation of Related Structures:  
    6MA1, 6MA2, 6MA3, 6MA4, 6MA5

  • PubMed Abstract: 

    Reversible glycosylation of nuclear and cytoplasmic proteins is an important regulatory mechanism across metazoans. One enzyme, O-linked N-acetylglucosamine transferase (OGT), is responsible for all nucleocytoplasmic glycosylation and there is a well-known need for potent, cell-permeable inhibitors to interrogate OGT function. Here we report the structure-based evolution of OGT inhibitors culminating in compounds with low nanomolar inhibitory potency and on-target cellular activity. In addition to disclosing useful OGT inhibitors, the structures we report provide insight into how to inhibit glycosyltransferases, a family of enzymes that has been notoriously refractory to inhibitor development.


  • Organizational Affiliation

    Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit723Homo sapiensMutation(s): 0 
Gene Names: OGT
EC: 2.4.1.255
UniProt & NIH Common Fund Data Resources
Find proteins for O15294 (Homo sapiens)
Explore O15294 
Go to UniProtKB:  O15294
GTEx:  ENSG00000147162 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15294
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Host Cell Factor 1 peptide16Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P51610 (Homo sapiens)
Explore P51610 
Go to UniProtKB:  P51610
GTEx:  ENSG00000172534 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51610
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JA4 (Subject of Investigation/LOI)
Query on JA4

Download Ideal Coordinates CCD File 
C [auth A]N-[(2R)-2-{[(7-chloro-2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}-2-(2-methoxyphenyl)acetyl]-N-[(thiophen-2-yl)methyl]glycine
C25 H22 Cl N3 O7 S2
AZINZNCYZJSBMU-XMMPIXPASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.303α = 90
b = 100.303β = 90
c = 130.301γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094263

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description