3D8Z

RNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine complex

Summary for 3D8Z

• Entry DOI: 10.2210/pdb3d8z/pdb
• Related: 3D8Y
• Descriptor: Ribonuclease pancreatic, 1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione, CITRATE ANION, ... (4 entities in total)
• Functional Keywords: ribonuclease, hydrolase, ligand binding, endonuclease, glycation, glycoprotein, nuclease, secreted
• Biological source: Bos taurus (Bovine)
• Cellular location: Secreted: P61823
• Total number of polymer chains: 2
• Total formula weight: 27901.09

Authors

Leonidas, D.D.,Zographos, S.E.,Oikonomakos, N.G. (deposition date: 2008-05-26, release date: 2009-02-10, Last modification date: 2024-11-13)

Primary citation

Samanta, A.,Leonidas, D.D.,Dasgupta, S.,Pathak, T.,Zographos, S.E.,Oikonomakos, N.G.
Morpholino, piperidino, and pyrrolidino derivatives of pyrimidine nucleosides as inhibitors of ribonuclease A: synthesis, biochemical, and crystallographic evaluation
J.Med.Chem., 52:932-942, 2009

PubMed Abstract: Six 5'-deoxy-5'-morpholine, piperidine, and pyrrolidine of pyrimidine nucleosides have been synthesized and characterized. Their inhibitory action to ribonuclease A has been studied by biochemical analysis and X-ray crystallography. These compounds are moderate inhibitors of RNase A with mid-to-upper micromolar inhibition constants (K(i)). The high resolution X-ray crystal structures of the RNase A-inhibitor complexes have shown that all inhibitors bind at the enzyme catalytic cleft with the pyrimidine nucleobase at the B(1)R(2) subsites while the 5' group binds away from the main subsite P(1), where P-O(5') bond cleavage occurs, toward the solvent close to subsite P(0). Structure-activity relationship analysis has demonstrated that the compounds with the larger group in the 5' position are more potent. Comparative structural analysis of these RNase A complexes with other similar RNase A-ligand complexes provides a structural explanation of their potency and suggests ways to improve their efficiency and selectivity. These inhibitors can be the starting point for the development of compounds that can be used as pharmaceuticals against pathologies associated with RNase A homologues such as human angiogenin, which is implicated in tumor induced neovascularization.

PubMed: 19173562
DOI: 10.1021/jm800724t

Experimental method

X-RAY DIFFRACTION (1.98 Å)