7NB3

Crystal structure of human choline alpha in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 

Starting Model: experimental
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Literature

Identification of unprecedented ATP-competitive choline kinase inhibitors.

Quartieri, F.Nesi, M.Avanzi, N.R.Borghi, D.Casale, E.Corti, E.Cucchi, U.Donati, D.Fasolini, M.Felder, E.R.Galvani, A.Giorgini, M.L.Lomolino, A.Menichincheri, M.Orrenius, C.Perrera, C.Re Depaolini, S.Riccardi-Sirtori, F.Salsi, E.Isacchi, A.Gnocchi, P.

(2021) Bioorg Med Chem Lett 51: 128310-128310

  • DOI: https://doi.org/10.1016/j.bmcl.2021.128310
  • Primary Citation of Related Structures:  
    7NB1, 7NB2, 7NB3

  • PubMed Abstract: 

    In this article we describe the identification of unprecedented ATP-competitive ChoKα inhibitors starting from initial hit NMS-P830 that binds to ChoKα in an ATP concentration-dependent manner. This result is confirmed by the co-crystal structure of NMS-P830 in complex with Δ75-ChoKα. NMS-P830 is able to inhibit ChoKα in cells resulting in the reduction of intracellular phosphocholine formation. A structure-based medicinal chemistry program resulted in the identification of selective compounds that have good biochemical activity, solubility and metabolic stability and are suitable for further optimization. The ChoKα inhibitors disclosed in this article demonstrate for the first time the possibility to inhibit ChoKα with ATP-competitive compounds.


  • Organizational Affiliation

    Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy. Electronic address: francesca.quartieri@nervianoms.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Choline kinase alphaA [auth AAA],
B [auth BBB]
384Homo sapiensMutation(s): 0 
Gene Names: CHKACHKCKI
EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P35790 (Homo sapiens)
Go to UniProtKB:  P35790
PHAROS:  P35790
GTEx:  ENSG00000110721 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U6H (Subject of Investigation/LOI)
Query on U6H

Download Ideal Coordinates CCD File 
C [auth AAA],
G [auth BBB]
4-(6-azanyl-2-pyridin-4-yl-purin-9-yl)-~{N}-(3-methoxyphenyl)cyclohexane-1-carboxamide
C24 H25 N7 O2
JLJXNSYNQKBEKE-MAEOIBBWSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
E [auth AAA],
F [auth AAA],
I [auth BBB]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth AAA],
H [auth BBB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
U6H BindingDB:  7NB3 IC50: 410 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.926α = 90
b = 120.199β = 90
c = 131.187γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description