6PVE

Structure of Nicotinamide N-Methyltransferase (NNMT) in complex with inhibitor LL319


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Novel Propargyl-Linked Bisubstrate Analogues as Tight-Binding Inhibitors for NicotinamideN-Methyltransferase.

Chen, D.Li, L.Diaz, K.Iyamu, I.D.Yadav, R.Noinaj, N.Huang, R.

(2019) J Med Chem 62: 10783-10797

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01255
  • Primary Citation of Related Structures:  
    6PVE, 6PVS

  • PubMed Abstract: 

    Nicotinamide N -methyltransferase (NNMT) catalyzes the methyl transfer from the cofactor S -adenosylmethionine to nicotinamide and other pyridine-containing compounds. NNMT is an important regulator for nicotinamide metabolism and methylation potential. Aberrant expression levels of NNMT have been implicated in cancer, metabolic, and neurodegenerative diseases, which makes NNMT a potential therapeutic target. Therefore, potent and selective NNMT inhibitors can serve as valuable tools to investigate the roles of NNMT in its mediated diseases. Here, we applied a rational strategy to design and synthesize the tight-binding bisubstrate inhibitor LL320 through a novel propargyl linker. LL320 demonstrates a K i value of 1.6 ± 0.3 nM, which is the most potent inhibitor to date. The cocrystal structure of LL320 confirms its interaction with both the substrate and cofactor binding sites on NNMT. Importantly, this is the first example of using the propargyl linker to construct potent methyltransferase inhibitors, which will expand our understanding of the transition state of methyl transfer.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NNMT protein
A, B, C, D
283Homo sapiensMutation(s): 3 
Gene Names: NNMThCG_39357
EC: 2.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P40261 (Homo sapiens)
Explore P40261 
Go to UniProtKB:  P40261
PHAROS:  P40261
GTEx:  ENSG00000166741 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40261
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.901α = 91.781
b = 62.359β = 97.608
c = 107.858γ = 111.555
Software Package:
Software NamePurpose
PHENIXrefinement
JBluIce-EPICSdata collection
HKL-2000data reduction
HKL-2000data scaling
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 States1R01GM127896-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM127884-01A1
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI127793
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM117275
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesU01CA214649-01

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2019-12-25
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Refinement description