2XOI

Functional and Structural Analyses of N-Acylsulfonamide-Linked Dinucleoside Inhibitors of Ribonuclease A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Functional and Structural Analyses of N-Acylsulfonamide-Linked Dinucleoside Inhibitors of Ribonuclease A.

Thiyagarajan, N., Smith, B.D., Raines, R.T., Ravi Acharya, K.

(2011) FEBS J 278: 541

  • DOI: 10.1111/j.1742-4658.2010.07976.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Molecular probes are useful for both studying and controlling the functions of enzymes and other proteins. The most useful probes have high affinity for their target, along with small size and resistance to degradation. Here, we report on new surroga ...

    Molecular probes are useful for both studying and controlling the functions of enzymes and other proteins. The most useful probes have high affinity for their target, along with small size and resistance to degradation. Here, we report on new surrogates for nucleic acids that fulfill these criteria. Isosteres in which phosphoryl [R-O-P(O(2)(-))-O-R'] groups are replaced with N-acylsulfonamidyl [R-C(O)-N(-)-S(O(2))-R'] or sulfonimidyl [R-S(O(2))-N(-)-S(O(2))-R'] groups increase the number of nonbridging oxygens from two (phosphoryl) to three (N-acylsulfonamidyl) or four (sulfonimidyl). Six such isosteres were found to be more potent inhibitors of catalysis by bovine pancreatic RNase A than are parent compounds containing phosphoryl groups. The atomic structures of two RNase A·N-acylsulfonamide complexes were determined at high resolution by X-ray crystallography. The N-acylsulfonamidyl groups were observed to form more hydrogen bonds with active site residues than did the phosphoryl groups in analogous complexes. These data encourage the further development and use of N-acylsulfonamides and sulfonimides as antagonists of nucleic acid-binding proteins.

    Organizational Affiliation: 

    Department of Biology and Biochemistry, University of Bath, UK.



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: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P61823 (Bos taurus)
Go to UniProtKB:  P61823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFB
Query on SFB
Download CCD File 
A, B
(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-N-[[(2S,3S,4R,5R)-5-(2,4-DIOXOPYRIMIDIN-1-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]METHYLSULFONYL]-3,4-DIHYDROXY-OXOLANE-2-CARBOXAMIDE
C20 H28 N8 O11 S
KEQMCGJHYDWPEW-ZSIUBJGCSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SFBKi:  460000   nM  PDBBind
SFBKi:  370000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.787α = 90
b = 33.146β = 90.94
c = 72.748γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance