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 

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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
  • Primary Citation of Related Structures:  
    2XOG, 2XOI

  • 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 surrogates for nucleic acids that fulfill these criteria ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE PANCREATICA, B124Bos taurusMutation(s): 0 
Gene Names: RNASE1, RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFB (Subject of Investigation/LOI)
Query on SFB
Download Ideal Coordinates CCD File 
C [auth A], D [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
SFB Binding MOAD:  2XOI Ki: 4.60e+5 (nM) from 1 assay(s)
PDBBind:  2XOI Ki: 4.60e+5 (nM) from 1 assay(s)
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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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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