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PDB ID Mentions in PubMed Central Article count: 2

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PDB ID Mentions in PubMed Central

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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

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).

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 structures (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.

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 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