Bovine Seminal Ribonuclease- Uridine 5' diphosphate complex

Experimental Data Snapshot

  • Resolution: 1.53 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Mapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors

Dossi, K.Tsirkone, V.G.Hayes, J.M.Matousek, J.Pouckova, P.Soucek, J.Zadinova, M.Zographos, S.E.Leonidas, D.D.

(2009) Eur J Med Chem 44: 4496-4508

  • DOI: https://doi.org/10.1016/j.ejmech.2009.06.039
  • Primary Citation of Related Structures:  
    3DJO, 3DJP, 3DJQ, 3DJV, 3DJX

  • PubMed Abstract: 

    Bovine seminal ribonuclease (BS-RNase) is a 27kDa homodimeric enzyme and a member of the pancreatic RNase A superfamily. It is the only RNase with a quaternary structure and it is a mixture of two dimeric forms. In the most abundant form the active site is formed by the swapping of the N-terminal segments. BS-RNase is a potent antitumor agent with severe side effects such as aspermatogenicity, and immunosuppression. As a first step towards the design of potent inhibitors of this enzyme we mapped its active site through the study of the binding of uridine 2'-phosphate (U2'p), uridine 3'-phosphate (U3'p), uridine 5'-diphosphate (UDP), cytidine 3'-phosphate (C3'p), and cytidine 5-phosphate (C5'p), by kinetics, and X-ray crystallography. These phosphonucleotides are potent inhibitors with C3'p being the most potent with a K(i) value of 22 microM. Absorption, distribution, metabolism, and excretion pharmacokinetic property predictions reveal U2'p, U3'p, and C5'p as the most promising with respect to oral bioavailability. In vivo studies on the aspermatogenic effect have shown that C3'p and C5'p inhibit significantly this biological action of BS-RNase.

  • Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Seminal ribonuclease
A, B
124Bos taurusMutation(s): 0 
Find proteins for P00669 (Bos taurus)
Explore P00669 
Go to UniProtKB:  P00669
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00669
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
UDP BindingDB:  3DJQ Ki: 1.05e+6 (nM) from 1 assay(s)
PDBBind:  3DJQ Ki: 1.05e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.53 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.08α = 90
b = 59.206β = 90
c = 82.723γ = 90
Software Package:
Software NamePurpose
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description