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 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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.

(2018) Bioorg Med Chem Lett 28: 437-440

  • DOI: 10.1016/j.bmcl.2017.12.023
  • Primary Citation of Related Structures:  
    5WI0, 5WI1

  • 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 potencies ...

    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. Electronic address: andrew.petros@abbvie.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferaseA, B491Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AQ1 (Subject of Investigation/LOI)
Query on AQ1

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]2-[(2-fluorophenyl)amino]-6-propylpyrimidin-4(3H)-one
C13 H14 F N3 O
PKDFHRREPYQILX-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AQ1 Binding MOAD:  5WI0 IC50: 3.60e+5 (nM) from 1 assay(s)
BindingDB:  5WI0 IC50: 3.60e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.226α = 90
b = 106.856β = 96.83
c = 82.881γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Data collection
  • Version 1.2: 2019-05-01
    Changes: Data collection, Database references