7BLE

Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with the tricyclic inhibitor (3)

PDB DOI: https://doi.org/10.2210/pdb7BLE/pdb

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

Deposited: 2021-01-18 Released: 2021-03-17
Deposition Author(s): Schreuder, H.A., Liesum, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.270
R-Value Work: 0.186
R-Value Observed: 0.191

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 128.21 kDa
Atom Count: 8,460
Modelled Residue Count: 1,032
Deposited Residue Count: 1,132
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40261
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
U1W (Subject of Investigation/LOI) Query on U1W Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth D] SDF format, chain F [auth A] SDF format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C]	F [auth A], H [auth B], J [auth C], L [auth D]	3-ethyl-1,3-diazatricyclo[6.3.1.0^{4,12}]dodeca-4,6,8(12)-trien-2-imine C₁₂ H₁₅ N₃ PBCCOMRKDASFBZ-OUKQBFOZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]