6B75

Crystal Structure of human NAMPT in complex with NVP-LOQ594

• PDB DOI: https://doi.org/10.2210/pdb6B75/pdb

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


• Deposited: 2017-10-03 Released: 2018-10-03 
• Deposition Author(s): Weihofen, W.A., Thigale, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.247 
• R-Value Work: 0.177 
• R-Value Observed: 0.181 

Literature

Identification and structure based design of cellularly active cyclo-propyl carboxamide Nicotinamide phosphoribosyltransferase (NAMPT) inhibitors

Palacios, D., Meredith, E., Kawanami, T., Adams, C., Chen, X., Darsigny, V., Geno, E., Palermo, M., Guy, C., Hewett, J., Tierney, L., THigale, S., Weihofen, W.A., Agrikar, U., Boynton, G., George, E., Wang, L.

To be published.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 229.15 kDa 
• Atom Count: 15,724 
• Modelled Residue Count: 1,865 
• Deposited Residue Count: 2,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B, C, D	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CVP	E [auth A], F [auth B], G [auth D]	4-[(piperazin-1-yl)methyl]-N-{[4-({[(pyridin-3-yl)methyl]carbamoyl}amino)phenyl]methyl}benzamide C26 H30 N6 O2 UPQVXXVUUYBILK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.247 
• R-Value Work: 0.177 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.049	α = 90
b = 207.985	β = 90
c = 98.466	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Weihofen, W.A., Thigale, S.

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description