8DSM | pdb_00008dsm

Human NAMPT in complex with inhibitor ZN-4-3

PDB DOI: https://doi.org/10.2210/pdb8DSM/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-22 Released: 2023-08-02
Deposition Author(s): Ratia, K., Xiong, R., Shen, Z., Thatcher, G.R.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.238 (Depositor), 0.237 (DCC)
R-Value Work:
0.194 (Depositor), 0.197 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A structural mechanism for positive allosteric modulation of nicotinamide phosphoribosyltransferase to elevate cellular NAD+

Ratia, K., Xiong, R., Shen, Z., Thatcher, G.R.

To be published.

Macromolecule Content

Total Structure Weight: 230.06 kDa
Atom Count: 15,222
Modeled Residue Count: 1,874
Deposited Residue Count: 1,996
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B, C, D	499	Homo sapiens	Mutation(s): 0 Gene Names: NAMPT, PBEF, PBEF1 EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens) Explore P43490 Go to UniProtKB: P43490
PHAROS: P43490 GTEx: ENSG00000105835
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TK0 (Subject of Investigation/LOI) Query on TK0 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain J [auth B]	E [auth A], J [auth B], L [auth C], O [auth D]	(3S)-N-[(1-benzothiophen-5-yl)methyl]-1-[6-(4-{2-[(2E)-3-(pyridin-3-yl)prop-2-enamido]ethyl}phenyl)thieno[2,3-d]pyrimidin-4-yl]piperidine-3-carboxamide C₃₇ H₃₄ N₆ O₂ S₂ XNJMWNJMIWAGCW-CRZWDPOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B], M [auth C], P [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain I [auth A] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain I [auth A] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain I [auth A]	I [auth A], Q [auth D], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain I [auth A] Focus chain Q [auth D] Focus chain R [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth C] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth C] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth C] mmCIF format, chain G [auth A]	G [auth A], H [auth A], N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth C]