4H4B

Human cytosolic 5'-nucleotidase II in complex with Anthraquinone-2,6- disulfonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification and characterization of inhibitors of cytoplasmic 5'-nucleotidase cN-II issued from virtual screening.

Jordheim, L.P.Marton, Z.Rhimi, M.Cros-Perrial, E.Lionne, C.Peyrottes, S.Dumontet, C.Aghajari, N.Chaloin, L.

(2013) Biochem Pharmacol 85: 497-506

  • DOI: 10.1016/j.bcp.2012.11.024
  • Primary Citation of Related Structures:  
    4H4B

  • PubMed Abstract: 
  • Clinical and preclinical observations have lead to the hypothesis that 5'-nucleotidase cN-II could constitute a therapeutic target in oncology, either per se or to increase the activity of cytotoxic nucleoside analogs. To identify potential cN-II inhibitors, we performed in silico screening of freely available chemical databases, in vitro enzymatic assays with recombinant cN-II, soaking experiments with crystals of truncated cN-II as well as biological evaluation of selected compounds, alone or in combination with cytotoxic nucleoside analogs, on cancer cells ...

    Clinical and preclinical observations have lead to the hypothesis that 5'-nucleotidase cN-II could constitute a therapeutic target in oncology, either per se or to increase the activity of cytotoxic nucleoside analogs. To identify potential cN-II inhibitors, we performed in silico screening of freely available chemical databases, in vitro enzymatic assays with recombinant cN-II, soaking experiments with crystals of truncated cN-II as well as biological evaluation of selected compounds, alone or in combination with cytotoxic nucleoside analogs, on cancer cells. The top ranked compounds from virtual screening included an anthraquinone derivative (AdiS) that were shown to block the enzyme activity with a K(i) of 2.0mM. Soaking experiments performed with crystals of truncated cN-II allowed to obtain crystallographic data at a resolution of 2.9 Å and indicating interaction between AdiS and F354/I152 situated in the effector site 1 of cN-II. In addition, this compound exhibited different levels of cytotoxicity in vitro on several cancer cell lines and increased the induction of apoptosis in RL cells incubated with 0.5 or 1.5 μM cladribine, 0.05 μM clofarabine or 30 μM fludarabine. Finally, AdiS showed synergy with cladribine and additivity with clofarabine. This study showed that virtual screening is a useful tool for the identification of potent cN-II inhibitors, and our biological results indicated interesting activity for one lead compound that can be further developed as therapeutics.


    Organizational Affiliation

    Université de Lyon, F-69000 Lyon, France. lars-petter.jordheim@univ-lyon1.fr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytosolic purine 5'-nucleotidaseA555Homo sapiensMutation(s): 0 
Gene Names: NT5C2NT5BNT5CPPNT5
EC: 3.1.3.5
UniProt & NIH Common Fund Data Resources
Find proteins for P49902 (Homo sapiens)
Explore P49902 
Go to UniProtKB:  P49902
PHAROS:  P49902
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
11H
Query on 11H

Download Ideal Coordinates CCD File 
B [auth A]9,10-dioxo-9,10-dihydroanthracene-2,6-disulfonic acid
C14 H8 O8 S2
MSSUFHMGCXOVBZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
11HKi :  2000000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.11α = 90
b = 126.83β = 90
c = 130.4γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-02-13
    Changes: Database references