6ATB | pdb_00006atb

Crystal Structure of human NAMPT in complex with NVP-LOD812

PDB DOI: https://doi.org/10.2210/pdb6ATB/pdb

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

Deposited: 2017-08-28 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:
0.215 (Depositor), 0.211 (DCC)
R-Value Work:
0.152 (Depositor), 0.151 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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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: 230.23 kDa
Atom Count: 16,259
Modeled Residue Count: 1,870
Deposited Residue Count: 2,004
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BWA (Subject of Investigation/LOI) Query on BWA Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain Q [auth D] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], L [auth C], Q [auth D]	N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-N'-[(pyridin-3-yl)methyl]urea C₂₂ H₁₈ N₄ O₃ KKBVILNJYCRNQY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], O [auth C], P [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain P [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], M [auth C], N [auth C], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]