Three-dimensional structure of the large cytoplasmic H 4 ?H 5 loop of Na + /K + -ATPase deduced by restraint-based comparative modeling shows only one ATP binding site

2001 ◽  
Vol 7 (6) ◽  
pp. 184-192 ◽  
Author(s):  
Jan Teisinger ◽  
Katerina Hofbauerova ◽  
Peter Kvasnicka ◽  
Wilhelm Schoner ◽  
Evzen Amler ◽  
...  
Keyword(s):  
Binding Site ◽  
Three Dimensional ◽  
Comparative Modeling ◽  
Dimensional Structure ◽  
Atp Binding ◽  
Three Dimensional Structure ◽  
Atp Binding Site

The three-dimensional structure of MAP kinase p38β: different features of the ATP-binding site in p38β compared with p38α

2009 ◽  
Vol 65 (8) ◽  
pp. 777-785 ◽  
Author(s):  
Sangita B. Patel ◽  
Patricia M. Cameron ◽  
Stephen J. O'Keefe ◽  
Betsy Frantz-Wattley ◽  
Jed Thompson ◽  
...  
Keyword(s):  
Map Kinase ◽  
Binding Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Atp Binding ◽  
Three Dimensional Structure ◽  
Atp Binding Site

THE THREE-DIMENSIONAL STRUCTURE OF THE ANTIGEN BINDING SITE OF McPC 603 PROTEIN

1974 ◽  
pp. 7-14 ◽  
Author(s):  
E.A. Padlan ◽  
D.M. Segal ◽  
G.H. Cohen ◽  
D.R. Davies ◽  
S. Rudikoff ◽  
...  
Keyword(s):  
Binding Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Antigen Binding ◽  
Antigen Binding Site ◽  
Three Dimensional Structure

scholarly journals Comparative modeling of the H4-H5 loop of the α2-isoform of Na+/K+-ATPase α-subunit in the E1 conformation

2007 ◽  
pp. S143-S151
Author(s):  
G Tejral ◽  
L Koláčná ◽  
A Kotyk ◽  
E Amler
Keyword(s):  
Binding Site ◽  
Phosphorylation Site ◽  
Comparative Modeling ◽  
Atp Binding ◽  
Beta Sheet ◽  
Alpha Helices ◽  
Α Subunit ◽  
Atp Binding Site ◽  
P Domain ◽  
Alpha Carbon

Restraint-based comparative modeling was used for calculation and visualization of the H4-H5-loop of Na+/K+-ATPase from mouse brain (Mus musculus, adult male brain, alpha2-isoform) between the amino acid residues Cys 336 and Arg 758 in the E1 conformation The structure consists of two well separated parts. The N-domain is formed by a seven-stranded antiparallel beta-sheet with two additional beta-strands and five alpha-helices sandwiching it, the P-domain is composed of a typical Rossman fold. The ATP-binding site was found on the N-domain to be identical in both alpha2- and alpha1-isoforms. The phosphorylation Asp 369 residue was found in the central part of the P-domain, located at the C-terminal end of the central beta-sheet. The distance between the alpha-carbon of Phe 475 at the ATP-binding site and the alpha-carbon of Asp 369 at the phosphorylation site is 3.22 nm. A hydrogen bond between the oxygen atom of Asp 369 and the nitrogen atom of Lys 690 was clearly detected and assumed to play a key role in maintaining the proper structure of the phosphorylaton site in E1 conformation.

scholarly journals A novel protein descriptor for the prediction of drug binding sites

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mingjian Jiang ◽  
Zhen Li ◽  
Yujie Bian ◽  
Zhiqiang Wei
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Three Dimensional ◽  
Drug Binding ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Site Prediction ◽  
Drug Binding Sites ◽  
Protein Descriptor ◽  
Novel Protein

Abstract Background Binding sites are the pockets of proteins that can bind drugs; the discovery of these pockets is a critical step in drug design. With the help of computers, protein pockets prediction can save manpower and financial resources. Results In this paper, a novel protein descriptor for the prediction of binding sites is proposed. Information on non-bonded interactions in the three-dimensional structure of a protein is captured by a combination of geometry-based and energy-based methods. Moreover, due to the rapid development of deep learning, all binding features are extracted to generate three-dimensional grids that are fed into a convolution neural network. Two datasets were introduced into the experiment. The sc-PDB dataset was used for descriptor extraction and binding site prediction, and the PDBbind dataset was used only for testing and verification of the generalization of the method. The comparison with previous methods shows that the proposed descriptor is effective in predicting the binding sites. Conclusions A new protein descriptor is proposed for the prediction of the drug binding sites of proteins. This method combines the three-dimensional structure of a protein and non-bonded interactions with small molecules to involve important factors influencing the formation of binding site. Analysis of the experiments indicates that the descriptor is robust for site prediction.

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure

1988 ◽  
Vol 31 (4) ◽  
pp. 722-729 ◽  
Author(s):  
Renee L. DesJarlais ◽  
Robert P. Sheridan ◽  
George L. Seibel ◽  
J. Scott Dixon ◽  
Irwin D. Kuntz ◽  
...  
Keyword(s):  
Binding Site ◽  
Receptor Binding ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Receptor Binding Site ◽  
Three Dimensional Structure ◽  
Shape Complementarity
Sign in / Sign up

Export Citation Format

Share Document