7SOK | pdb_00007sok

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.245 (Depositor), 0.246 (DCC)
R-Value Work:
0.207 (Depositor), 0.208 (DCC)
R-Value Observed:
0.208 (Depositor)

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

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40261
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9XL Query on 9XL Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain E [auth C] MOL2 format, chain P [auth D] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain E [auth C] mmCIF format, chain P [auth D] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain E [auth C]	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		Interactions Focus chain E [auth C] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth D] Interactions & Density Focus chain E [auth C] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain F [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain F [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain F [auth C]	F [auth C] G [auth C] H [auth C] I [auth C] J [auth C] 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		Interactions Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.245 (Depositor), 0.246 (DCC)
R-Value Work: 0.207 (Depositor), 0.208 (DCC)
R-Value Observed: 0.208 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-02

Deposition Author(s):

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