4P5D

CRYSTAL STRUCTURE OF RAT DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE-MONOPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: Synthesis, structural studies and cytotoxic activities.

Amiable, C.Paoletti, J.Haouz, A.Padilla, A.Labesse, G.Kaminski, P.A.Pochet, S.

(2014) Eur.J.Med.Chem. 85C: 418-437

  • DOI: 10.1016/j.ejmech.2014.07.110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) has been proposed as a new molecular target for cancer treatment. Here, we describe the synthesis of a series of novel 6-aryl- and 6-heteroarylpurine riboside 5'-monophosphates via Suzuki-Miya ...

    The 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) has been proposed as a new molecular target for cancer treatment. Here, we describe the synthesis of a series of novel 6-aryl- and 6-heteroarylpurine riboside 5'-monophosphates via Suzuki-Miyaura cross-coupling reactions, and their ability to inhibit recombinant rat and human DNPH1. Enzymatic inhibition studies revealed competitive inhibitors in the low micromolar range. Crystal structures of human and rat DNPH1 in complex with one nucleotide from this series, the 6-naphthylpurine derivative, provided detailed structural information, in particular regarding the possible conformations of a long and flexible loop wrapping around the large hydrophobic substituent. Taking advantage of these high-resolution structures, we performed virtual docking studies in order to evaluate enzyme-inhibitor interactions for the whole compound series. Among the synthesized compounds, several molecules exhibited significant in vitro cytotoxicity against human colon cancer (HCT15, HCT116) and human promyelocytic leukemia (HL60) cell lines with IC50 values in the low micromolar range, which correlated with in vitro DNPH1 inhibitory potency.


    Related Citations: 
    • Structure of the oncoprotein Rcl bound to three nucleotide analogues.
      Padilla, A.,Amiable, C.,Pochet, S.,Kaminski, P.A.,Labesse, G.
      (2013) Acta Crystallogr. D Biol. Crystallogr. 69: 247


    Organizational Affiliation

    Institut Pasteur, Unité de Chimie et Biocatalyse, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; CNRS, UMR3523, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2'-deoxynucleoside 5'-phosphate N-hydrolase 1
C, A
152Rattus norvegicusMutation(s): 1 
Gene Names: Dnph1 (Rcl)
EC: 3.2.2.-
Find proteins for O35820 (Rattus norvegicus)
Go to UniProtKB:  O35820
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
N6P
Query on N6P

Download SDF File 
Download CCD File 
A, C
6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine
6-Naphthylpurine riboside 5'-monophosphate
C20 H19 N4 O7 P
LQGRESLLVHYRLI-VXXKDZQQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N6PKi: 1500 nM (99) BINDINGDB
N6PKi: 1500 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.175 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 178.200α = 90.00
b = 178.200β = 90.00
c = 56.922γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release