6MA5 | pdb_00006ma5

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

• PDB DOI: https://doi.org/10.2210/pdb6MA5/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-25 Released: 2018-10-17 
• Deposition Author(s): Martin, S.E.S., Lazarus, M.B., Walker, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

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

• PubMed: 30285435 
• DOI: https://doi.org/10.1021/jacs.8b07328
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States.
Division of Preclinical Innovation, National Center for Advancing Translational Sciences , National Institutes of Health , Bethesda , Maryland 20892 , United States.
Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.
Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.
The David H. Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.
Department of Pharmacological Sciences , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.12 kDa 
• Atom Count: 6,056 
• Modeled Residue Count: 711 
• Deposited Residue Count: 739 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A	723	Homo sapiens	Mutation(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
PHAROS:  O15294 GTEx:  ENSG00000147162

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Host Cell Factor 1 peptide	B	16	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P51610 (Homo sapiens) Explore P51610  Go to UniProtKB:  P51610
PHAROS:  P51610 GTEx:  ENSG00000172534

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J9V (Subject of Investigation/LOI)	C [auth A]	N-[(2R)-2-(2-methoxyphenyl)-2-{[(2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}acetyl]-N-[(thiophen-2-yl)methyl]glycine C25 H23 N3 O7 S2 OIUMFGYEVQJCBR-XMMPIXPASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.79	α = 90
b = 98.79	β = 90
c = 365.91	γ = 120

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Martin, S.E.S., Lazarus, M.B., Walker, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094263

Revision History  

• 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