6B75 | pdb_00006b75

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free:
0.247 (Depositor), 0.254 (DCC)
R-Value Work:
0.177 (Depositor), 0.181 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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: 229.15 kDa
Atom Count: 15,724
Modeled Residue Count: 1,865
Deposited Residue Count: 2,004
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CVP Query on CVP Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.247 (Depositor), 0.254 (DCC)
R-Value Work: 0.177 (Depositor), 0.181 (DCC)
R-Value Observed: 0.181 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2018-10-03

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.