Crystal structure of NAMPT bound to ligand TSY535(compound 9a)

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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Chemistry-led investigations into the mode of action of NAMPT activators, resulting in the discovery of non-pyridyl class NAMPT activators.

Tang, S.Garzon Sanz, M.Smith, O.Kramer, A.Egbase, D.Caton, P.W.Knapp, S.Butterworth, S.

(2023) Acta Pharm Sin B 13: 709-721

  • DOI: https://doi.org/10.1016/j.apsb.2022.07.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The cofactor nicotinamide adenine dinucleotide (NAD + ) plays a key role in a wide range of physiological processes and maintaining or enhancing NAD + levels is an established approach to enhancing healthy aging. Recently, several classes of nicotinamide phosphoribosyl transferase (NAMPT) activators have been shown to increase NAD +  levels in vitro and in vivo and to demonstrate beneficial effects in animal models. The best validated of these compounds are structurally related to known urea-type NAMPT inhibitors, however the basis for the switch from inhibitory activity to activation is not well understood. Here we report an evaluation of the structure activity relationships of NAMPT activators by designing, synthesising and testing compounds from other NAMPT ligand chemotypes and mimetics of putative phosphoribosylated adducts of known activators. The results of these studies led us to hypothesise that these activators act via a through-water interaction in the NAMPT active site, resulting in the design of the first known urea-class NAMPT activator that does not utilise a pyridine-like warhead, which shows similar or greater activity as a NAMPT activator in biochemical and cellular assays relative to known analogues.

  • Organizational Affiliation

    Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PL, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B
497Mus musculusMutation(s): 0 
Gene Names: NamptPbef1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99KQ4 (Mus musculus)
Explore Q99KQ4 
Go to UniProtKB:  Q99KQ4
IMPC:  MGI:1929865
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99KQ4
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.101α = 90
b = 108.253β = 97.16
c = 83.693γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
The Structural Genomics Consortium (SGC)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-01-31
    Changes: Refinement description