7NB2 | pdb_00007nb2

Crystal structure of human choline alpha in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.248 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.202 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7NB2

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 91.57 kDa 
  • Atom Count: 5,870 
  • Modeled Residue Count: 699 
  • Deposited Residue Count: 768 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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)
Explore P35790 
Go to UniProtKB:  P35790
PHAROS:  P35790
GTEx:  ENSG00000110721 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35790
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U6E
(Subject of Investigation/LOI)

Query on U6E



Download:Ideal Coordinates CCD File
E [auth AAA],
H [auth BBB]
4-(6-azanyl-2-chloranyl-purin-9-yl)-~{N}-(4-methyl-1,3-thiazol-2-yl)cyclohexane-1-carboxamide
C16 H18 Cl N7 O S
JIOZKGZDCQTDDN-AOOOYVTPSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
C [auth AAA],
D [auth AAA],
G [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
F [auth AAA],
I [auth BBB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
U6E BindingDB:  7NB2 IC50: 49 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.248 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.593α = 90
b = 120.926β = 90
c = 130.456γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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