9H4Z | pdb_00009h4z

NNMT-SAM IN COMPLEX WITH 3b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 
    0.217 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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Literature

Mechanism and kinetics of turnover inhibitors of nicotinamide N-methyl transferase in vitro and in vivo.

Akerud, T.De Fusco, C.Brandt, P.Bergstrom, F.Johansson, P.Ek, M.Borjesson, U.Johansson, A.Danielsson, J.Bauer, M.Arnaud, B.Castaldo, M.Stromstedt, M.Rosengren, B.Jansen, F.Fredlund, L.

(2025) J Biological Chem 301: 108492-108492

  • DOI: https://doi.org/10.1016/j.jbc.2025.108492
  • Primary Citation of Related Structures:  
    9GVM, 9GVW, 9GWA, 9H4Z, 9H5E, 9H5O

  • PubMed Abstract: 

    Nicotinamide N-methyl transferase (NNMT) is involved in the regulation of cellular nicotinamide adenine dinucleotide (NAD) and S-Adenosyl-L-methionine (SAM) levels and has been implicated in a range of human diseases. Herein, we show that a class of NNMT inhibitors; analogues of the natural substrate nicotinamide (NAM) are turned over by the enzyme and that the methylated product is a potent inhibitor of the enzyme. The product inhibitor is, however, charged and has modest cellular potency. Utilizing this on-target biotransformation combines the cell permeability of the substrate with the high potency of the product that results in highly efficient inhibition in vivo. First we studied the structure-activity-relationship for both substrates and methylated products and solved structures using X-ray crystallography of representative inhibitors. Then we designed a new surface biosensor method to understand the structure-kinetic-relationship for the inhibitors. We were able to quantify the substrate binding kinetics to NNMT-SAM, catalysis rate and rate of product release from NNMT-SAH in a single experiment. This is to our knowledge the first time an enzyme surface biosensor has been used to study and quantify catalysis in detail. Finally, by monitoring plasma concentrations of turnover inhibitor substrate, product and the endogenous product, 1-Methyl nicotinamide (1-MNA), in the rat, we show that the turnover inhibitor mechanism of action is relevant in vivo.


  • Organizational Affiliation
    • Protein, Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden. Electronic address: tomas.akerud@astrazeneca.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide N-methyltransferaseA [auth B],
B [auth D]
280Homo sapiensMutation(s): 3 
Gene Names: NNMT
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: 1.41 Å
  • R-Value Free:  0.217 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.01α = 90
b = 69.72β = 90
c = 115.19γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XSCALEdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release