4P5E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


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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:  
    4P5D, 4P5E

  • 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-Miyaura cross-coupling reactions, and their ability to inhibit recombinant rat and human DNPH1 ...

    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. Electronic address: sylvie.pochet@pasteur.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2'-deoxynucleoside 5'-phosphate N-hydrolase 1A, B152Homo sapiensMutation(s): 0 
Gene Names: DNPH1C6orf108RCL
EC: 3.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for O43598 (Homo sapiens)
Explore O43598 
Go to UniProtKB:  O43598
PHAROS:  O43598
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N6P
Query on N6P

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine
C20 H19 N4 O7 P
LQGRESLLVHYRLI-VXXKDZQQSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N6PKi:  1500   nM  BindingDB
N6PKi:  2800   nM  Binding MOAD
N6PKi:  2800   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.974α = 90
b = 52.284β = 104.77
c = 54.454γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Infrastructure for Integrated Structural BiologyFranceANR-10-INSB-05-01

Revision History  (Full details and data files)

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