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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
Development and validation of an improved algorithm for overlaying flexible molecules.
(2012) J Comput Aided Mol Des 26
PubMed: 22538643 | PubMedCentral: PMC3348445 | DOI: 10.1007/s10822-012-9573-y
14 True overlay of ten heat shock protein ligands, showing the poor volume overlap of three ligands (from PDB complexes 1byq, 1uy8, 1yet, coloured in magenta ) with the remainder (1yc1, 1yc4,... 2bsm, 2byi, 2bz5, 2cct, 2uwd, coloured in green ) Acetylcholinesterase This is the only protein on which we were entirely unsuccessful.
Table 1 Test sets Protein Number of complexes PDB codes Protein kinase 5 (PK5) 2 1v0o, 1v0p Fatty acid binding protein (FABP) 3 1tou, 1tow, 2hnx Neprilysin (NEP) 4 1dmt, 1r1h, 1r1j, 1y8j Dihydrofolate reductase (DHFR) 6 1drf, 1hfr, 1mvt, 1pd9, 1s3v, 2dhf Checkpoint kinase (Chk1) 16 1nvq, 1nvr, 1nvs, 1zlt, 1zys, 2br1, 2brb, 2brg, 2brh, 2brm, 2bro, 2c3l, 2cgu, 2cgw, 2cgx, 2hog Neuraminidase (NEU) 11 1a4g, 1a4q, 1b9s, 1b9t, 1b9v, 1inf, 1inv, 1ivb, 1nsc, 1nsd, 1vcj Carbonic anhydrase (CA) 13 1bn3, 1bn4, 1bnq, 1cim, 1eou, 1if7, 1oq5, 1xpz, 1zgf, 1zh9, 2eu3, 2hoc, 2nng Adenosine deaminase (ADA) 11 1krm, 1ndv, 1ndw, 1ndy, 1o5r, 1qxl, 1uml, 1v7a, 1v79, 1wxy, 2e1w Heat shock protein 90 (HSP) 10 1byq, 1uy8, 1yc1, 1yc4, 1yet, 2bsm, 2byi, 2bz5, 2cct, 2uwd Acetylcholinesterase (AChE) 11 1dx6, 1e66, 1eve, 1gpk, 1gpn, 1h23, 1w4l, 1zgb, 2ack, 2c5g, 2ckm Table 2 Test subsets Protein/subset Number of complexes PDB codes ADA/1 10 1ndv, 1ndw, 1ndy, 1o5r, 1qxl, 1uml, 1v7a, 1v79, 1wxy, 2e1w ADA/2 4 1o5r, 1qxl, 1uml, 1wxy ADA/3 4 1ndv, 1o5r, 1qxl, 1uml HSP/1 7 1yc1, 1yc4, 2bsm, 2byi, 2bz5, 2cct, 2uwd HSP/2 3 1byq, 1uy8, 2cct AChE/1 9 1dx6, 1e66, 1gpk, 1gpn, 1h23, 1w4l, 1zgb, 2ack, 2ckm AChE/2 4 1h23, 1w4l, 1zgb, 2ckm Ligand models were created with CORINA [ 38 ] with addition of required hydrogen atoms.
Heat shock protein 90 The 10 ligands in this set may be divided into two groups: (a) the closely similar pyrazole or isoxazole ligands of 1yc1, 1yc4, 2bsm, 2byi, 2bz5, 2cct, 2uwd together with the structurally unrelated ligand from 2bz5; and (b) two purine ligands (1byq and 1uy8) and the macrocyclic ligand from 1yet.
Publication Year: 2012
Co-crystalization and in vitro biological characterization of 5-aryl-4-(5-substituted-2-4-dihydroxyphenyl)-1,2,3-thiadiazole Hsp90 inhibitors.
(2012) PLoS One 7
PubMed: 22984537 | PubMedCentral: PMC3439374 | DOI: 10.1371/journal.pone.0044642
The structure was solved by molecular replacement with Phaser using pdb code 2WI1 for compounds ICPD 26, and 47, and PDB code 1YC1 for ICPD 34 as the search model.
Identification of two novel HSP90 proteins in Babesia orientalis: molecular characterization, and computational analyses of their structure, function, antigenicity and inhibitor interaction.
(2014) Parasit Vectors 7
PubMed: 24970594 | PubMedCentral: PMC4089566 | DOI: 10.1186/1756-3305-7-293
Table 2 Interaction of Babesia orientalis HSP90-A and B isoforms with inhibitors using docking analysis Name Protein showing interaction Template ID PDB code Geldanamycin BoHSP90-A, BoHSP90-B Gmy1 2ex... Radamide BoHSP90-A, BoHSP90-B Rda1001 2gfd Redicicol BoHSP90-A, BoHSP90-B Rdc301 1u0z Dihydroxyphenylpyrazoles BoHSP90-A, BoHSP90-B 4BC401 1yc1 PU8(8-(2-chloro-3,4,5-trimethoxy-benzyl)-2-fluoro-9-pent-4-ylnyl-9 h-purin-6-ylamine) BoHSP90-B PU11224 1uyf PU11 (8-(2,5-dimethoxy-benzyl)-2-fluoro-9- pent-9 h-purin-6-ylamine) BoHSP90-A Puz1224 1uyi 1-(2-phenol)-2-naphthol BoHSP90-A, BoHSP90-B AB41226 2bz5 3,4-diaryl pyrazole resorcinol (CCT018159) BoHSP90-A, BoHSP90-B Ct51224 2bt0 4-amino derivative of 3,4-diaryl pyrazole (4-chloro-6-(4-piperazin-1-yl-1 h-pyrazol-3-yl)-benzene-1,2-diol) BoHSP90-B 4BH1224 2ccs The template IDs are the identification numbers of inhibitors in RCSB Protein Data Bank.
Publication Year: 2014
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