7BKG

Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with the tricyclic inhibitor (2)

• PDB DOI: https://doi.org/10.2210/pdb7BKG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-01-15 Released: 2021-03-17 
• Deposition Author(s): Schreuder, H.A., Liesum, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.236 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Literature

Novel Inhibitors of Nicotinamide- N -Methyltransferase for the Treatment of Metabolic Disorders.

Kannt, A., Rajagopal, S., Hallur, M.S., Swamy, I., Kristam, R., Dhakshinamoorthy, S., Czech, J., Zech, G., Schreuder, H., Ruf, S.

(2021) Molecules 26

• PubMed: 33668468 
• DOI: https://doi.org/10.3390/molecules26040991
• Primary Citation of Related Structures:  
  7BKG, 7BLE, 7NBJ, 7NBM, 7NBQ


• PubMed Abstract: 
  

  Nicotinamide- N -methyltransferase (NNMT) is a cytosolic enzyme catalyzing the transfer of a methyl group from S -adenosyl-methionine (SAM) to nicotinamide (Nam). It is expressed in many tissues including the liver, adipose tissue, and skeletal muscle. Its expression in several cancer cell lines has been widely discussed in the literature, and recent work established a link between NNMT expression and metabolic diseases. Here we describe our approach to identify potent small molecule inhibitors of NNMT featuring different binding modes as elucidated by X-ray crystallographic studies.

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Organizational Affiliation: 

Fraunhofer Institute for Translational Medicine and Pharmacology-ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 128.16 kDa 
• Atom Count: 8,994 
• Modelled Residue Count: 1,050 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide N-methyltransferase	A, B, C, D	283	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], G [auth B], I [auth C], K [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
U0Z (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	5,6-dihydro-2-imino-2H,4H-thiazolo(5,4,3-IJ)quinoline C10 H10 N2 S JHKKLXTWYNAHPM-ZHACJKMWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.236 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.935	α = 91.64
b = 62.304	β = 98.25
c = 107.61	γ = 111.64

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Schreuder, H.A., Liesum, A.

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description