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Scoring functions and enrichment: a case study on Hsp90.

(2007) BMC Bioinformatics 8

PubMed: 17257425 | PubMedCentral: PMC1790905 | DOI: 10.1186/1471-2105-8-27

Protonation states as at pH7, atom- and bond-types, hydrogen addition, and consideration of active site waters for inclusion/exclusion were implemented using SYBYL ® 7.0 for the crystal struct... res (PDB Codes: 1YC1 / 1YC3 / 1YC4 [ 29 ], 1BYQ [ 30 ]) containing the ligands 4BC (Figure 1 ), 43P (Figure 1 ), and ADP bound to the N-terminal ATP binding domain of human Hsp90α.

Results and discussion We analysed crystal structures (PDB Codes: 1YC1 / 1YC3 / 1YC4 [ 29 ], 1BYQ [ 30 ]) containing the ligands 4BC (Figure 1 ), 43P (Figure 1 ), and ADP (Figure 2 ) bound to the N-terminal ATP binding domain of human Hsp90α, as described in detail in the Methods section.

Table 1 Deviations between docked and crystallographic conformations Compounds GOLD ChemScore 4BC (no tether) 1.84 [ 1YC1 ] /0.38 [ 1YC3 ] 1.19 [ 1YC1 ]/ 1.58 [ 1YC3 ] 4BC (Thrl84) 1.

62 [ 1YC1 ] /0.51 [ 1YC3 ] 0.71 [ 1YC1 ] /0.98 [ 1YC3 ] 43P (no tether) 0.51 [ 1YC4 ] 0.64 [ 1YC4 ] 43P (Thrl84) 0.78 [ 1YC4 ] 1.19 [ 1YC4 ] RMS deviations in Å between the docked conformations of ' active ' compounds 4BC and 43P and their corresponding crystallographic conformations (PDB codes: 1YC1 , 1YC3 , 1YC4 ).

The RMSD was calculated between each docked ligand and its later published crystallographic conformation (PDB Codes: 1YC1 / 1YC3 / 1YC4 ) (Table 1 and Figures 3 , 4).

The RMSD values between the docked ligands and their crystallographic conformations (1YC1/1YC3/1YC4) are given in Table 1 .

Publication Year: 2007