5NSD

Co-crystal structure of NAMPT dimer with KPT-9274


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.046 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Target identification of small molecules using large-scale CRISPR-Cas mutagenesis scanning of essential genes.

Neggers, J.E.Kwanten, B.Dierckx, T.Noguchi, H.Voet, A.Bral, L.Minner, K.Massant, B.Kint, N.Delforge, M.Vercruysse, T.Baloglu, E.Senapedis, W.Jacquemyn, M.Daelemans, D.

(2018) Nat Commun 9: 502-502

  • DOI: 10.1038/s41467-017-02349-8

  • PubMed Abstract: 
  • Unraveling the mechanism of action and molecular target of small molecules remains a major challenge in drug discovery. While many cancer drugs target genetic vulnerabilities, loss-of-function screens fail to identify essential genes in drug mechanis ...

    Unraveling the mechanism of action and molecular target of small molecules remains a major challenge in drug discovery. While many cancer drugs target genetic vulnerabilities, loss-of-function screens fail to identify essential genes in drug mechanism of action. Here, we report CRISPRres, a CRISPR-Cas-based genetic screening approach to rapidly derive and identify drug resistance mutations in essential genes. It exploits the local genetic variation created by CRISPR-Cas-induced non-homologous end-joining (NHEJ) repair to generate a wide variety of functional in-frame mutations. Using large sgRNA tiling libraries and known drug-target pairs, we validate it as a target identification approach. We apply CRISPRres to the anticancer agent KPT-9274 and identify nicotinamide phosphoribosyltransferase (NAMPT) as its main target. These results present a powerful and simple genetic approach to create many protein variants that, in combination with positive selection, can be applied to reveal the cellular target of small-molecule inhibitors.


    Organizational Affiliation

    KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000, Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinamide phosphoribosyltransferase
A, B
497Homo sapiensMutation(s): 0 
Gene Names: NAMPT (PBEF, PBEF1)
EC: 2.4.2.12
Find proteins for P43490 (Homo sapiens)
Go to Gene View: NAMPT
Go to UniProtKB:  P43490
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
96Q
Query on 96Q

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Download CCD File 
A, B
(~{E})-3-(6-azanylpyridin-3-yl)-~{N}-[[5-[4-[4,4-bis(fluoranyl)piperidin-1-yl]carbonylphenyl]-7-(4-fluorophenyl)-1-benzofuran-2-yl]methyl]prop-2-enamide
C35 H29 F3 N4 O3
MRFOPLWJZULAQD-SWGQDTFXSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.046 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.138α = 90.00
b = 109.167β = 96.63
c = 84.974γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Database references