6AZJ

Crystal Structure of human NAMPT in complex with NVP-LQN520

PDB DOI: https://doi.org/10.2210/pdb6AZJ/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-09-11 Released: 2018-09-12
Deposition Author(s): Weihofen, W.A., Thigale, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.229
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 113.26 kDa
Atom Count: 7,790
Modelled Residue Count: 929
Deposited Residue Count: 990
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B	495	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C5V (Subject of Investigation/LOI) Query on C5V Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	(1S,2S)-N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-2-(pyridin-3-yl)cyclopropane-1-carboxamide C₂₄ H₁₉ N₃ O₃ ZFFWKXDUNGUFER-RTWAWAEBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
C5V	BindingDB: 6AZJ	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.229
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.23	α = 90
b = 157.72	β = 90
c = 192.18	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-09-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-09-12
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.