5U2M

Crystal structure of human NAMPT with A-1293201

• PDB DOI:  https://doi.org/10.2210/pdb5U2M/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Mammalia
• Mutation(s): No 


• Deposited: 2016-11-30 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: 1.89 Å
• R-Value Free: 0.220 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Discovery and Characterization of Novel Nonsubstrate and Substrate NAMPT Inhibitors.

Wilsbacher, J.L., Cheng, M., Cheng, D., Trammell, S.A.J., Shi, Y., Guo, J., Koeniger, S.L., Kovar, P.J., He, Y., Selvaraju, S., Heyman, H.R., Sorensen, B.K., Clark, R.F., Hansen, T.M., Longenecker, K.L., Raich, D., Korepanova, A.V., Cepa, S., Towne, D.L., Abraham, V.C., Tang, H., Richardson, P.L., McLoughlin, S.M., Badagnani, I., Curtin, M.L., Michaelides, M.R., Maag, D., Buchanan, F.G., Chiang, G.G., Gao, W., Rosenberg, S.H., Brenner, C., Tse, C.

(2017) Mol Cancer Ther 16: 1236-1245

• PubMed: 28468779 
• DOI: https://doi.org/10.1158/1535-7163.MCT-16-0819
• Primary Citation of Related Structures:  
  5U2M, 5U2N


• PubMed Abstract: 
  

Cancer cells are highly reliant on NAD ⁺ -dependent processes, including glucose metabolism, calcium signaling, DNA repair, and regulation of gene expression. Nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme for NAD ⁺ salvage from nicotinamide, has been investigated as a target for anticancer therapy. Known NAMPT inhibitors with potent cell activity are composed of a nitrogen-containing aromatic group, which is phosphoribosylated by the enzyme. Here, we identified two novel types of NAM-competitive NAMPT inhibitors, only one of which contains a modifiable, aromatic nitrogen that could be a phosphoribosyl acceptor. Both types of compound effectively deplete cellular NAD ⁺ , and subsequently ATP, and produce cell death when NAMPT is inhibited in cultured cells for more than 48 hours. Careful characterization of the kinetics of NAMPT inhibition in vivo allowed us to optimize dosing to produce sufficient NAD ⁺ depletion over time that resulted in efficacy in an HCT116 xenograft model. Our data demonstrate that direct phosphoribosylation of competitive inhibitors by the NAMPT enzyme is not required for potent in vitro cellular activity or in vivo antitumor efficacy. Mol Cancer Ther; 16(7); 1236-45. ©2017 AACR .

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Organizational Affiliation: 

AbbVie Inc., North Chicago, Illinois.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 109.55 kDa 
• Atom Count: 8,129 
• Modelled Residue Count: 928 
• Deposited Residue Count: 954 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	477	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7T7	C [auth A], G [auth B]	N-[4-({[(3S)-oxolan-3-yl]methyl}carbamoyl)phenyl]-1,3-dihydro-2H-isoindole-2-carboxamide C21 H23 N3 O3 BLZJCPAXCWJANZ-HNNXBMFYSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
7T7	BindingDB:  5U2M	Ki: 24 (nM) from 1 assay(s)
		IC50: min: 19.7, max: 34.2 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.220 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.978	α = 90
b = 106.611	β = 96.64
c = 83.122	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
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