5WI0 | pdb_00005wi0

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

• PDB DOI: https://doi.org/10.2210/pdb5WI0/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-07-18 Released: 2018-01-10 
• Deposition Author(s): Longenecker, K.L., Raich, D., Korepanova, A.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

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

• PubMed: 29287958 
• DOI: https://doi.org/10.1016/j.bmcl.2017.12.023
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States.
Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 111.68 kDa 
• Atom Count: 8,087 
• Modeled Residue Count: 928 
• Deposited Residue Count: 982 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	491	Homo sapiens	Mutation(s): 0  Gene Names: NAMPT, PBEF, PBEF1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AQ1 (Subject of Investigation/LOI)	C [auth A], D [auth B]	2-[(2-fluorophenyl)amino]-6-propylpyrimidin-4(3H)-one C13 H14 F N3 O PKDFHRREPYQILX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AQ1	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 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.226	α = 90
b = 106.856	β = 96.83
c = 82.881	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Longenecker, K.L., Raich, D., Korepanova, A.V.

Revision History  

• 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
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description