8F7L

Human NAMPT in complex with substrate NAM and small molecule activator ZN-29-S

PDB DOI: https://doi.org/10.2210/pdb8F7L/pdb

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

Deposited: 2022-11-18 Released: 2023-11-29
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: 2.20 Å
R-Value Free: 0.264
R-Value Work: 0.226
R-Value Observed: 0.228

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Human NAMPT in complex with substrate NAM and small molecule activator ZN-29-S

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

To be published.

Macromolecule Content

Total Structure Weight: 114.8 kDa
Atom Count: 7,830
Modelled Residue Count: 938
Deposited Residue Count: 998
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 phosphoribosyltransferase	A, B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XI3 (Subject of Investigation/LOI) Query on XI3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	(3S)-N-[(1-benzothiophen-5-yl)methyl]-1-[(2P)-2-(3-fluoro-4-methylphenyl)-2H-pyrazolo[3,4-d]pyrimidin-4-yl]piperidine-3-carboxamide C₂₇ H₂₅ F N₆ O S LQSRIPAMJVTBAV-FQEVSTJZSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
NCA Query on NCA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	NICOTINAMIDE C₆ H₆ N₂ O DFPAKSUCGFBDDF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	D [auth A], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]