6E68 | pdb_00006e68

NAMPT co-crystal with inhibitor compound 2

• PDB DOI: https://doi.org/10.2210/pdb6E68/pdb

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


• Deposited: 2018-07-24 Released: 2018-08-08 
• Deposition Author(s): Waight, A.B., Neumann, C.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

NAMPT co-crystal with inhibitor compound 2

Neumann, C.S., Olivas, K.C., Anderson, M.E., Cochran, J.H., Jin, S., Li, F., Loftus, L.V., Meyer, D.W., Neale, J., Nix, J.C., Pittman, P.G., Simmons, J.K., Ulrich, M.L., Waight, A.B., Wong, A., Zaval, M.C., Zeng, W., Lyon, R.P., Senter, P.D.

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)

Macromolecule Content 

• Total Structure Weight: 109.99 kDa 
• Atom Count: 8,743 
• Modeled Residue Count: 940 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	480	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HVM (Subject of Investigation/LOI)	D [auth A], F [auth B]	(2E)-N-{4-[1-(3-aminobenzene-1-carbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide C24 H30 N4 O2 JLAJCUOAEWKJJS-MDZDMXLPSA-N
PO4	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.464	α = 90
b = 106.41	β = 96.55
c = 82.745	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Waight, A.B., Neumann, C.S.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description