5WI0

Crystal structure of human NAMPT with fragment 2: 2-[(2-fluorophenyl)amino]-6-propylpyrimidin-4(3H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-based discovery of a potent NAMPT inhibitor.

Korepanova, A.Longenecker, K.L.Pratt, S.D.Panchal, S.C.Clark, R.F.Lake, M.Gopalakrishnan, S.M.Raich, D.Sun, C.Petros, A.M.

(2017) Bioorg. Med. Chem. Lett. --: --

  • DOI: 10.1016/j.bmcl.2017.12.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NAMPT expression is elevated in many cancers, making this protein a potential target for anticancer therapy. We have carried out both NMR based and TR-FRET based fragment screens against human NAMPT and identified six novel binders with a range of po ...

    NAMPT expression is elevated in many cancers, making this protein a potential target for anticancer therapy. We have carried out both NMR based and TR-FRET based fragment screens against human NAMPT and identified six novel binders with a range of potencies. Co-crystal structures were obtained for two of the fragments bound to NAMPT while for the other four fragments force-field driven docking was employed to generate a bound pose. Based on structural insights arising from comparison of the bound fragment poses to that of bound FK866 we were able to synthetically elaborate one of the fragments into a potent NAMPT inhibitor.


    Organizational Affiliation

    Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide phosphoribosyltransferase
A, B
491Homo sapiensMutation(s): 0 
Gene Names: NAMPT (PBEF, PBEF1)
EC: 2.4.2.12
Find proteins for P43490 (Homo sapiens)
Go to Gene View: NAMPT
Go to UniProtKB:  P43490
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AQ1
Query on AQ1

Download SDF File 
Download CCD File 
A, B
2-[(2-fluorophenyl)amino]-6-propylpyrimidin-4(3H)-one
C13 H14 F N3 O
PKDFHRREPYQILX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.226α = 90.00
b = 106.856β = 96.83
c = 82.881γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-03-21
    Type: Data collection