5U2N

Crystal structure of human NAMPT with A-1326133


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery and Characterization of Novel Nonsubstrate and Substrate NAMPT Inhibitors.

Wilsbacher, J.L.Cheng, M.Cheng, D.Trammell, S.A.J.Shi, Y.Guo, J.Koeniger, S.L.Kovar, P.J.He, Y.Selvaraju, S.Heyman, H.R.Sorensen, B.K.Clark, R.F.Hansen, T.M.Longenecker, K.L.Raich, D.Korepanova, A.V.Cepa, S.Towne, D.L.Abraham, V.C.Tang, H.Richardson, P.L.McLoughlin, S.M.Badagnani, I.Curtin, M.L.Michaelides, M.R.Maag, D.Buchanan, F.G.Chiang, G.G.Gao, W.Rosenberg, S.H.Brenner, C.Tse, C.

(2017) Mol Cancer Ther 16: 1236-1245

  • DOI: https://doi.org/10.1158/1535-7163.MCT-16-0819
  • Primary Citation of Related Structures:  
    5U2M, 5U2N

  • PubMed Abstract: 

    Cancer cells are highly reliant on NAD + -dependent processes, including glucose metabolism, calcium signaling, DNA repair, and regulation of gene expression. Nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme for NAD + salvage from nicotinamide, has been investigated as a target for anticancer therapy. Known NAMPT inhibitors with potent cell activity are composed of a nitrogen-containing aromatic group, which is phosphoribosylated by the enzyme. Here, we identified two novel types of NAM-competitive NAMPT inhibitors, only one of which contains a modifiable, aromatic nitrogen that could be a phosphoribosyl acceptor. Both types of compound effectively deplete cellular NAD + , and subsequently ATP, and produce cell death when NAMPT is inhibited in cultured cells for more than 48 hours. Careful characterization of the kinetics of NAMPT inhibition in vivo allowed us to optimize dosing to produce sufficient NAD + depletion over time that resulted in efficacy in an HCT116 xenograft model. Our data demonstrate that direct phosphoribosylation of competitive inhibitors by the NAMPT enzyme is not required for potent in vitro cellular activity or in vivo antitumor efficacy. Mol Cancer Ther; 16(7); 1236-45. ©2017 AACR .


  • Organizational Affiliation

    AbbVie Inc., North Chicago, Illinois. julie.wilsbacher@abbvie.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B
477Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7TA
Query on 7TA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
N-{4-[1-(2-methylpropanoyl)piperidin-4-yl]phenyl}-2H-pyrrolo[3,4-c]pyridine-2-carboxamide
C23 H26 N4 O2
UXDAQOSAZJARDY-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.166α = 90
b = 107.049β = 96.77
c = 83.135γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2018-03-21
    Changes: Data collection
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description