4LTS | pdb_00004lts

Discovery of Potent and Efficacious Cyanoguanidine-containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4LTS/pdb

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


• Deposited: 2013-07-23 Released: 2013-12-25 
• Deposition Author(s): Zheng, X., Baumeister, T., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Han, B., Ho, Y., Kley, N., Lin, J., Reynoids, D.J., Sharma, G., Smith, C.C., Wang, Z., Dragovich, P.S., Oh, A., Wang, W., Zak, M., Wang, L., Yuen, P., Bair, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.190 (Depositor), 0.155 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Discovery of potent and efficacious cyanoguanidine-containing nicotinamide phosphoribosyltransferase (Nampt) inhibitors.

Zheng, X., Baumeister, T., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Han, B., Ho, Y.C., Kley, N., Lin, J., Reynolds, D.J., Sharma, G., Smith, C.C., Wang, Z., Dragovich, P.S., Oh, A., Wang, W., Zak, M., Wang, Y., Yuen, P.W., Bair, K.W.

(2014) Bioorg Med Chem Lett 24: 337-343

• PubMed: 24279990 
• DOI: https://doi.org/10.1016/j.bmcl.2013.11.006
• Primary Citation Related Structures: 
  4LTS, 4LWW


• PubMed Abstract: 
  

  A co-crystal structure of amide-containing compound (4) in complex with the nicotinamide phosphoribosyltransferase (Nampt) protein and molecular modeling were utilized to design and discover a potent novel cyanoguanidine-containing inhibitor bearing a sulfone moiety (5, Nampt Biochemical IC50=2.5nM, A2780 cell proliferation IC50=9.7nM). Further SAR exploration identified several additional cyanoguanidine-containing compounds with high potency and good microsomal stability. Among these, compound 15 was selected for in vivo profiling and demonstrated good oral exposure in mice. It also exhibited excellent in vivo antitumor efficacy when dosed orally in an A2780 ovarian tumor xenograft model. The co-crystal structure of this compound in complex with the NAMPT protein was also determined.

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Organizational Affiliation: 
• Forma Therapeutics, Inc., 500 Arsenal Street, Watertown, MA 02472, USA. Electronic address: [e-mail].
Forma Therapeutics, Inc., 500 Arsenal Street, Watertown, MA 02472, USA.
Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
Pharmaron Beijing, Co. Ltd, 6 Tai He Road, BDA, Beijing 100176, PR China.

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: 115.58 kDa 
• Atom Count: 8,672 
• Modeled Residue Count: 945 
• Deposited Residue Count: 1,002 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	501	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LTS	C [auth A], I [auth B]	2-cyano-1-pyridin-4-yl-3-(4-{[3-(trifluoromethoxy)phenyl]sulfonyl}benzyl)guanidine C21 H16 F3 N5 O3 S OSHZYJJYBZWSLR-UHFFFAOYSA-N
PO4	D [auth A], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LTS	BindingDB:  4LTS	IC50: 6.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.190 (Depositor), 0.155 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.782	α = 90
b = 106.314	β = 96.55
c = 82.94	γ = 90

Software Package:

Software Name	Purpose
B3	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Zheng, X., Baumeister, T., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Han, B., Ho, Y., Kley, N., Lin, J., Reynoids, D.J., Sharma, G., Smith, C.C., Wang, Z., Dragovich, P.S., Oh, A., Wang, W., Zak, M., Wang, L., Yuen, P., Bair, K.W.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description