2G8R

The crystal structure of the RNase A- 3-N-piperidine-4-carboxyl-3-deoxy-ara-uridine complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The binding of 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine to ribonuclease A in the crystal.

Leonidas, D.D.Maiti, T.K.Samanta, A.Dasgupta, S.Pathak, T.Zographos, S.E.Oikonomakos, N.G.

(2006) Bioorg.Med.Chem. 14: 6055-6064

  • DOI: 10.1016/j.bmc.2006.05.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The binding of a moderate inhibitor, 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine, to ribonuclease A has been studied by X-ray crystallography at 1.7A resolution. Two inhibitor molecules are bound in the central RNA binding cavity of RNase A explo ...

    The binding of a moderate inhibitor, 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine, to ribonuclease A has been studied by X-ray crystallography at 1.7A resolution. Two inhibitor molecules are bound in the central RNA binding cavity of RNase A exploiting interactions with residues from peripheral binding sites rather than from the active site of the enzyme. The uracyl moiety of the first inhibitor molecule occupies the purine-preferring site of RNase A, while the rest of the molecule projects to the solvent. The second inhibitor molecule binds with the carboxyl group at the pyrimidine recognition site and the uridine moiety exploits interactions with RNase A residues Lys66, His119 and Asp121. Comparative structural analysis of the 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine complex with other RNase A-ligand complexes provides a structural explanation of its potency. The crystal structure of the RNase A-3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine complex provides evidence of a novel ligand-binding pattern in RNase A for 3'-N-aminonucleosides that was not anticipated by modelling studies, while it also suggests ways to improve the efficiency and selectivity of such compounds to develop pharmaceuticals against pathologies associated with RNase A homologues.


    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece. ddl@eie.gr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease pancreatic
A, B
124Bos taurusMutation(s): 0 
Gene Names: RNASE1 (RNS1)
EC: 4.6.1.18
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N3E
Query on N3E

Download SDF File 
Download CCD File 
A
1-[3-(4-CARBOXYPIPERIDIN-1-YL)-3-DEOXY-BETA-D-ARABINOFURANOSYL]PYRIMIDINE-2,4(1H,3H)-DIONE
3-N-PIPERIDINE-4-CARBOXYL-3-DEOXY-ARA-URIDINE
C15 H21 N3 O7
IBEGWFLXVPJKRI-FOUMNBMASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N3EKi: 103000 nM BINDINGMOAD
N3EKi: 103000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.174α = 90.00
b = 32.530β = 90.46
c = 72.512γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance