5UPE

Crystal structure of human NAMPT with isoindoline urea inhibitor compound 5

• PDB DOI: https://doi.org/10.2210/pdb5UPE/pdb

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


• Deposited: 2017-02-02 Released: 2017-06-28 
• Deposition Author(s): Longenecker, K.L., Raich, D., Korepanova, A.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.217 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

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

• PubMed: 28610984 
• 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.

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Organizational Affiliation: 

AbbVie Inc, 1 North Waukegan Rd., North Chicago, IL 60064, United States. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 113.98 kDa 
• Atom Count: 8,099 
• Modelled Residue Count: 928 
• Deposited Residue Count: 998 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	499	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
8HY	C [auth A], D [auth B]	N-{4-[(3-phenylpropyl)carbamoyl]phenyl}-2H-isoindole-2-carboxamide C25 H23 N3 O2 YXCPDCLETYPTMF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8HY	Binding MOAD:  5UPE	Ki: 9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.217 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.073	α = 90
b = 106.448	β = 96.63
c = 83.109	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
autoPROC	data scaling
2016	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Longenecker, K.L., Raich, D., Korepanova, A.V.

Revision History  

• 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