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: 116.21 kDa 
• Atom Count: 8,671 
• Modelled Residue Count: 939 
• Deposited Residue Count: 1,002 
• Unique protein chains: 1

 4LVA

Fragment-based Identification of Amides Derived From trans-2-(Pyridin-3-yl)cyclopropanecarboxylic Acid as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)

• PDB DOI:  https://doi.org/10.2210/pdb4LVA/pdb

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


• Deposited: 2013-07-26 Released: 2013-09-25 
• Deposition Author(s): Giannetti, A.M., Zheng, X., Skelton, N., Wang, W., Bravo, B., Feng, Y., Gunzner-Toste, J., Ho, Y., Hua, R., Wang, C., Zhao, Q., Liederer, B.M., Liu, Y., O'Brien, T., Oeh, J., Sampath, D., Shen, Y., Wang, L., Wu, H., Xiao, Y., Yuen, P., Zak, M., Zhao, G., Dragovich, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.207 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

Identification of amides derived from 1H-pyrazolo[3,4-b]pyridine-5-carboxylic acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT).

Zheng, X., Bair, K.W., Bauer, P., Baumeister, T., Bowman, K.K., Buckmelter, A.J., Caligiuri, M., Clodfelter, K.H., Feng, Y., Han, B., Ho, Y.C., Kley, N., Li, H., Liang, X., Liederer, B.M., Lin, J., Ly, J., O'Brien, T., Oeh, J., Oh, A., Reynolds, D.J., Sampath, D., Sharma, G., Skelton, N., Smith, C.C., Tremayne, J., Wang, L., Wang, W., Wang, Z., Wu, H., Wu, J., Xiao, Y., Yang, G., Yuen, P.W., Zak, M., Dragovich, P.S.

(2013) Bioorg Med Chem Lett 23: 5488-5497

• PubMed: 24021463 
• DOI: https://doi.org/10.1016/j.bmcl.2013.08.074
• Primary Citation of Related Structures:  
  4LV9, 4LVA, 4LVB, 4LVD, 4LVF, 4LVG, 4M6P, 4M6Q


• PubMed Abstract: 
  

Potent, 1H-pyrazolo[3,4-b]pyridine-containing inhibitors of the human nicotinamide phosphoribosyltransferase (NAMPT) enzyme were identified using structure-based design techniques. Many of these compounds exhibited nanomolar antiproliferation activities against human tumor lines in in vitro cell culture experiments, and a representative example (compound 26) demonstrated encouraging in vivo efficacy in a mouse xenograft tumor model derived from the A2780 cell line. This molecule also exhibited reduced rat retinal exposures relative to a previously studied imidazo-pyridine-containing NAMPT inhibitor. Somewhat surprisingly, compound 26 was only weakly active in vitro against mouse and monkey tumor cell lines even though it was a potent inhibitor of NAMPT enzymes derived from these species. The compound also exhibited only minimal effects on in vivo NAD levels in mice, and these changes were considerably less profound than those produced by an imidazo-pyridine-containing NAMPT inhibitor. The crystal structures of compound 26 and the corresponding PRPP-derived ribose adduct in complex with NAMPT were also obtained.

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Organizational Affiliation: 

Forma Therapeutics, Inc., 500 Arsenal Street, Watertown, MA 02472, USA.

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
20M	C [auth A], M [auth B]	N-(4-{[4-(pyrrolidin-1-yl)piperidin-1-yl]sulfonyl}benzyl)-2H-pyrido[4,3-e][1,2,4]thiadiazin-3-amine 1,1-dioxide C22 H28 N6 O4 S2 BCPZRYGPLBZKEZ-UHFFFAOYSA-N
PO4	D [auth A], E [auth A], F [auth A], N [auth B], O [auth B], P [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
20M	BindingDB:  4LVA	IC50: 62 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.207 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.511	α = 90
b = 106.799	β = 96.59
c = 83.04	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Giannetti, A.M., Zheng, X., Skelton, N., Wang, W., Bravo, B., Feng, Y., Gunzner-Toste, J., Ho, Y., Hua, R., Wang, C., Zhao, Q., Liederer, B.M., Liu, Y., O'Brien, T., Oeh, J., Sampath, D., Shen, Y., Wang, L., Wu, H., Xiao, Y., Yuen, P., Zak, M., Zhao, G., Dragovich, P.S.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary