8TM7 | pdb_00008tm7

Human NAMPT in complex with substrate NAM and small molecule activator NP-A3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.198 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.178 (Depositor) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8TM7

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Nicotinamide Phosphoribosyltransferase Positive Allosteric Modulators Attenuate Neuronal Oxidative Stress.

Gordon-Blake, J.Ratia, K.Weidig, V.Velma, G.R.Ackerman-Berrier, M.Penton, C.Musku, S.R.Alves, E.T.M.Driver, T.Tai, L.Thatcher, G.R.J.

(2024) ACS Med Chem Lett 15: 205-214

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00391
  • Primary Citation Related Structures: 
    8TM7

  • PubMed Abstract: 

    Evidence supports boosting nicotinamide adenine dinucleotide (NAD + ) to counteract oxidative stress in aging and neurodegenerative disease. One approach is to enhance the activity of nicotinamide phosphoribosyltransferase (NAMPT). Novel NAMPT positive allosteric modulators (N-PAMs) were identified. A cocrystal structure confirmed N-PAM binding to the NAMPT rear channel. Early hit-to-lead efforts led to a 1.88-fold maximum increase in the level of NAD + in human THP-1 cells. Select N-PAMs were assessed for mitigation of reactive oxygen species (ROS) in HT-22 neuronal cells subject to inflammatory stress using tumor necrosis factor alpha (TNFα). N-PAMs that increased NAD + more effectively in THP-1 cells attenuated TNFα-induced ROS more effectively in HT-22 cells. The most efficacious N-PAM completely attenuated ROS elevation in glutamate-stressed HT-22 cells, a model of neuronal excitotoxicity. This work demonstrates for the first time that N-PAMs are capable of mitigating elevated ROS in neurons stressed with TNFα and glutamate and provides support for further N-PAM optimization for treatment of neurodegenerative diseases.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, Research Resources Center, Department of Chemistry, and Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, Illinois 60612, United States.

Macromolecule Content 

  • Total Structure Weight: 114.88 kDa 
  • Atom Count: 7,988 
  • Modeled Residue Count: 934 
  • Deposited Residue Count: 998 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B
499Homo sapiensMutation(s): 0 
Gene Names: NAMPTPBEFPBEF1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43490
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I7Q
(Subject of Investigation/LOI)

Query on I7Q



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
N-{2-[(4R)-2,2-dimethyl-4-(propan-2-yl)oxan-4-yl]ethyl}-N-[(4-methoxyphenyl)methyl]furan-2-carboxamide
C25 H35 N O4
SQGCJJXFRGWDAL-RUZDIDTESA-N
NCA

Query on NCA



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B]
NICOTINAMIDE
C6 H6 N2 O
DFPAKSUCGFBDDF-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
J [auth A],
M [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.198 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.178 (Depositor) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.56α = 90
b = 106.864β = 96.71
c = 83.222γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesRF1AG067771

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release