7SOK

Structure of Nicotinamide N-Methyltransferase (NNMT) in complex with inhibitor II329

• PDB DOI: https://doi.org/10.2210/pdb7SOK/pdb

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


• Deposited: 2021-10-31 Released: 2022-11-02 
• Deposition Author(s): Yadav, R., Iyamu, I.D., Huang, R., Noinaj, N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.245 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Literature

Structure of Nicotinamide N-Methyltransferase (NNMT) in complex with inhibitor II329

Iyamu, I., Vilseck, J.Z., Yadav, R., Noinaj, N., Huang, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 128.88 kDa 
• Atom Count: 8,572 
• Modelled Residue Count: 1,038 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NNMT protein	A [auth C], B [auth A], C [auth B], D	283	Homo sapiens	Mutation(s): 3  Gene Names: NNMT, hCG_39357
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
9XL	E [auth C], K [auth A], N [auth B], P [auth D]	(2S)-2-amino-4-([3-(3-carbamoylphenyl)prop-2-yn-1-yl]{[(1R,2R,3S,4R)-4-(4-chloro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,3-dihydroxycyclopentyl]methyl}amino)butanoic acid C26 H29 Cl N6 O5 JIYDUPLVTSNGNC-BLCKVISQSA-N
PEG	F [auth C], G [auth C], H [auth C], I [auth C], J [auth C], L [auth A], M [auth A], O [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.245 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.821	α = 110.07
b = 62.596	β = 103.82
c = 79.781	γ = 103.85

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Yadav, R., Iyamu, I.D., Huang, R., Noinaj, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM127896-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM127884-01A1
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01AI127793
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01GM117275
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	U01CA214649-01

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description