5UPF

Crystal structure of human NAMPT with isoindoline urea inhibitor compound 53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

SAR and characterization of non-substrate isoindoline urea inhibitors of nicotinamide phosphoribosyltransferase (NAMPT).

Curtin, M.L.Heyman, H.R.Clark, R.F.Sorensen, B.K.Doherty, G.A.Hansen, T.M.Frey, R.R.Sarris, K.A.Aguirre, A.L.Shrestha, A.Tu, N.Woller, K.Pliushchev, M.A.Sweis, R.F.Cheng, M.Wilsbacher, J.L.Kovar, P.J.Guo, J.Cheng, D.Longenecker, K.L.Raich, D.Korepanova, A.V.Soni, N.B.Algire, M.A.Richardson, P.L.Marin, V.L.Badagnani, I.Vasudevan, A.Buchanan, F.G.Maag, D.Chiang, G.G.Tse, C.Michaelides, M.R.

(2017) Bioorg Med Chem Lett 27: 3317-3325

  • DOI: https://doi.org/10.1016/j.bmcl.2017.06.018
  • Primary Citation of Related Structures:  
    5UPE, 5UPF

  • PubMed Abstract: 

    Herein we disclose SAR studies that led to a series of isoindoline ureas which we recently reported were first-in-class, non-substrate nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. Modification of the isoindoline and/or the terminal functionality of screening hit 5 provided inhibitors such as 52 and 58 with nanomolar antiproliferative activity and preclinical pharmacokinetics properties which enabled potent antitumor activity when dosed orally in mouse xenograft models. X-ray crystal structures of two inhibitors bound in the NAMPT active-site are discussed.


  • Organizational Affiliation

    AbbVie Inc, 1 North Waukegan Rd., North Chicago, IL 60064, United States. Electronic address: mike.curtin@abbvie.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8HV
Query on 8HV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
5-fluoro-N-{4-[1-(2-hydroxy-2-methylpropanoyl)piperidin-4-yl]phenyl}-2H-isoindole-2-carboxamide
C24 H26 F N3 O3
XZCZXZPDNUPSAB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.104α = 90
b = 106.578β = 96.86
c = 83.337γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling
2016data reduction

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: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2018-03-21
    Changes: Data collection
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description