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PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Tamoxifen enhances the Hsp90 molecular chaperone ATPase activity.

(2010) PLoS One 5

PubMed: 20376192 | PubMedCentral: PMC2848575 | DOI: 10.1371/journal.pone.0009934

The top 15 scoring hits were 12 estrogen receptor structures and 3 Hsp90 structures (pdb codes 1uyf, 1uy8, and 2ior–see Table S1 ).

( A ) Conformation of 4-OHT (magenta) docked onto the crystal structure of the N-terminal ATP-binding domain of human Hsp90α (yellow mesh, pdb code 1uy8).

Unlike ADP, the 4-OHT aliphatic chain extends deep into the pocket, and makes multiple hydrophobic contacts with the lid which acts as a structural switch between the active (green–pdb code 2cg9) and inactive (red–pdb code 1uy8) conformation of the enzyme.

Raloxifene docked well to one of the Hsp90 structures (pdb code 1uyf), but not to the best 2 scoring structures for tamoxifen (pdb codes 2ior and 1uy8).

Publication Year: 2010

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

Hsp90 inhibitors, part 2: combining ligand-based and structure-based approaches for virtual screening application.

(2014) J Chem Inf Model 54

PubMed: 24555544 | PubMedCentral: PMC3985681 | DOI: 10.1021/ci400760a

Figure 3 The most active screened compounds in their BC system (protein and pose) overlapped with 2YK2( 16 ) (Hit 1 in orange, Hit 2 in cyan, protein in cyan): (A) NCI610930 in 1UYC (ligand and protei... in green), (B) NCI117285 in 1UY8 (ligand in yellow, protein in magenta), and (C) NCI170578 in 1UY8 (ligand and protein in magenta).

Table 1 RMSD and AA Values Calculated between the Random (RC) and Experimental Conformations (EC) in the Realignment and Cross-Alignment Processes (RCRA and RCCA, Respectively)     RCRA ECCA RCCA entry a PDB code RC vs EC EC vs all RC vs all 1 1UY8 0.46 0.37 0.52 2 1UYC 0.47 0.45 0.49 3 1UYD 0.7 0.36 0.43 4 1UYE 0.69 0.55 0.6 5 1UYG 0.41 0.74 0.65 6 1UYH 0.46 0.38 0.49 7 1UYK 0.62 0.26 0.56 13 2BT0 0.58 0.33 0.48 14 2CCS 0.46 0.64 0.74 16 2CCU 0.8 3.5 3.8 17 3B25 0.48 0.39 0.21 18 3B26 0.5 0.6 0.35 20 3B28 0.71 0.55 0.45 21 3OWB 0.65 0.74 0.7 22 3OWD 0.98 0.3 0.81           AA b   100 93.33 93.33 a Entry numbers are referred to those reported in Table 1 of reference ( 5 ) b Alignment accuracy, which refers to the fraction of correct and partially correct aligned structures (RMSD values of <2 Å and <3 Å, respectively), and it is explained by eq 1 .

Publication Year: 2014