4KXL

Crystal structure of DNPH1 (RCL) with 6-CYCLOPENTYL-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1.

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

(2013) Plos One 8: e80755-e80755

  • DOI: 10.1371/journal.pone.0080755
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The gene dnph1 (or rcl) encodes a hydrolase that cleaves the 2'-deoxyribonucleoside 5'-monophosphate (dNMP) N-glycosidic bond to yield a free nucleobase and 2-deoxyribose 5-phosphate. Recently, the crystal structure of rat DNPH1, a potential target f ...

    The gene dnph1 (or rcl) encodes a hydrolase that cleaves the 2'-deoxyribonucleoside 5'-monophosphate (dNMP) N-glycosidic bond to yield a free nucleobase and 2-deoxyribose 5-phosphate. Recently, the crystal structure of rat DNPH1, a potential target for anti-cancer therapies, suggested that various analogs of AMP may inhibit this enzyme. From this result, we asked whether N (6)-substituted AMPs, and among them, cytotoxic cytokinin riboside 5'-monophosphates, may inhibit DNPH1. Here, we characterized the structural and thermodynamic aspects of the interactions of these various analogs with DNPH1. Our results indicate that DNPH1 is inhibited by cytotoxic cytokinins at concentrations that inhibit cell growth.


    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.,Sect.D 69: 247


    Organizational Affiliation

    Institut Pasteur, Unité de Chimie et Biocatalyse, Paris, 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
A, B, C, D
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
6C6
Query on 6C6

Download SDF File 
Download CCD File 
A, B, C, D
N-cyclopentyladenosine 5'-(dihydrogen phosphate)
C15 H22 N5 O7 P
ZLXWBMMFOMQXRH-SDBHATRESA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6C6Ki: 1200 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 32.728α = 90.00
b = 100.644β = 101.79
c = 79.681γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release