Citations in PubMed

Primary Citation PubMed: 11349148 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Binding-site assessment by virtual fragment screening.

(2010) PLoS One 5

PubMed: 20404926 | PubMedCentral: PMC2852417 | DOI: 10.1371/journal.pone.0010109

Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) ACE 1uze 0.60 HIVRT 1vrt 1.66 1o86 0.17 0.37 0.4... 1rt1 1.51 2.45 1.75 1uzf 0.35 0.79 0.69 1c1c a 1.88 3.12 1.61 Alr2 1ah0 1.42 1rth a 1.62 2.28 1.61 1ah3 a 1.06 3.19 1.27 HMGR 1hw8 1.39 2acr a , b 0.88 1.72 1.10 1hwk 0.61 1.49 1.31 CDK2 1aq1 a 1.32 NA 1a4g 0.57 1buh a , b 1.77 3.20 1.44 1a4q a 0.48 2.11 0.52 1dm2 a 1.75 4.49 1.62 1nsc a 0.34 1.49 0.52 COX-2 1cvu 1.51 P38 MAPK 1a9u 1.00 1cx2 a 1.24 3.78 1.53 1kv1 3.84 10.41 1.16 3pgh a 1.11 3.96 1.64 1kv2 3.54 11.26 1.61 DHFR 3dfr 1.01 PDE5 1xoz 1.18 6dfr b 1.47 1.96 1.02 1xp0 0.79 2.23 1.24 ER 1l2i 1.69 PPARg 1fm6 1.46 3ert a 2.61 4.47 1.55 1fm9 a 1.47 4.64 1.62 1err a 2.01 4.39 1.61 2prg a 0.71 1.27 1.43 Fxa 1f0r 1.64 Thrombin 1ba8 1.53 1fjs 1.09 2.57 1.59 1hgt b 0.69 1.85 1.55 1ksn a 0.67 1.65 1.59 TK 1kim a 1.58 1xka a 1.27 2.46 1.56 1ki4 a 1.78 2.90 1.40 RMSD ave was defined as the sidechain RMSD based on binding site residues within a cutoff distance of 4.5 Å from crystallographic ligands; RMSD max is defined as the largest sidechain RMSD value among all the binding site residues.

Publication Year: 2010


Improving structural similarity based virtual screening using background knowledge.

(2013) J Cheminform 5

PubMed: 24341870 | PubMedCentral: PMC3928642 | DOI: 10.1186/1758-2946-5-50

In the PDB six co-crystallizations of HMGR are available, each with one statin: atorvastatin ([PDB:1HWK]), fluvastatin ([PDB:1HWI]), simvastatin ([PDB:1HW9]), compactin ([PDB:1HW8]), rosuvastatin ([PD... :1HWL]) and cerivastatin ([PDB:[1HWJ]).

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4170813

Table 1 Targets for SPLIF Benchmarking Collected from DUD-E class target description PDB actives a decoys a Gscore cutoff b refs kinase FAK1 focal adhesion kinase 1 3bz3 100 (71) 5350 ... 2131) –6.0 ( 9 ) (1mp8, 2etm, 2ijm, 3bz3, 4gu6, 4gu9, 4i4e, 4k8a, 4kab) AKT1 serine/threonine-protein kinase AKT 3cqw 293 (199) 16450 (6131) –5.0 ( 12 ) (3cqu, 3cqw, 3mv5, 3mvh, 3ocb, 3ow4, 3qkk, 3cql, 3qkm, 4ekk, 4ekl, 4gv1) protease ACE angiotensin-converting enzyme 3bkl 282 (277) 16900 (16454) –2.5 ( 13 ) (1o86, 1uze, 1uzf, 2c6n, 2oc2, 2xy9, 2xyd, 2ydm, 3bkk, 3bkl, 3l3n, 3nxq, 4bxk) TRYB1 tryptase beta-1 2zec 148 (59) 7650 (1657) –6.0 ( 5 ) (2f9p, 2f9n, 2zeb, 2zec, 4a6l) HMDH HMG-CoA reductase 3ccw 170 (170) 8750 (8456) –2.5 22 (1dq8, 1dq9, 1dqa, 1hw8, 1hw9, 1hwi, 1hwj, 1hwk, 1hwl, 2q1l, 2q6b, 2q6c, 2r4f, 3bgl, 3cct, 3ccw, 3ccz, 3cd0, 3cd5, 3cd7, 3cda, 3cdb) GPCR ADRB1 Beta-1 adrenergic receptor 2vt4 247 (240) 15842 (13932) –4.0 ( 14 ) (2vt4, 2y00, 2y01, 2y02, 2y03, 2y04, 2ycw, 2ycx, 2ycy, 2ycz, 3zpq, 3zpr, 4ami, 4amj) nuclear receptor MCR mineralocorticoid receptor 2aa2 94 (66) 5150 (2481) –6.0 ( 13 ) (2aa2, 1y9r, 1ya3, 2a3i, 2aa5, 2aa6, 2aa7, 2aax, 2ab2, 2abi, 2oax, 3vhu, 3vhv) PRGR progesterone receptor 3kba 293 (222) 15650 (12914) –5.0 ( 17 ) (1a28, 1e3k, 1sqn, 1sr7, 1zuc, 2ovh, 2ovm, 2w8y, 3d90, 3g8o, 3hq5, 3kba, 3zr7, 3zra, 3zrb, 4a2j, 4apu) ion channel GRIK1 glutamate receptor ionotropic kainate 1 1vso 101 (96) 6550 (5980) –2.5 ( 17 ) (1txf, 1vso, 1ycj, 2f34, 2f35, 2f36, 2pbw, 2qs1, 2qs2, 2qs3, 2qs4, 2wky, 3gba, 3gbb, 3s2v, 4dld, 4e0x) synthase PGH2 cyclooxygenase-2 3ln1 435 (374) 23150 (17948) –5.0 27 (1cvu, 1cx2, 1ddx, 1pxx, 3hs5, 3hs6, 3hs7, 3krk, 3ln0, 3ln1, 3mdl, 3nt1, 3ntb, 3ntg, 3olt, 3olu, 3pgh, 3q7d, 3qh0, 3qmq, 3rr3, 3tzi, 4cox, 4e1g, 4fm5, 4llz, 6cox) a Initial numbers of actives and decoys from DUD-E with the numbers after the Gscore filter included in parentheses.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4352280

Docking analysis Crystallographic structures used in this study for HMG-CoA reductase in complex with atorvastatin (PDB ID: 1HWK) was retrieved from the Research Collaboratory for Structural Bioinform... tics (RCSB) Protein Data Bank ( www.pdb.org ).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4492635

We used the 3D structure 1HWK from the PDB (Protein Data Bank) database of hHMGR as the target to screen for the strongly bound compounds from the traditional Chinese medicine database.

8 , 9 We selected the 3D structure of hHMGR (1HWK from PDB [Protein Data Bank]) as the target and virtually screened the Traditional Chinese Medicine (TCM) database for tightly bound compounds, using the molecular modeling tool.

Molecular docking and analysis of ligand-protein interactions The 3D structure PDB 1HWK 10 of hHMGR was chosen as the molecular target and obtained from the PDB ( http://www.rcsb.org/pdb ).

Results and discussion Virtual screening for human HMG-CoA reductase inhibitors The 3D structure of hHMGR (PDB 1HWK) was chosen as the molecular target of the present study.

Notes: ( A ) The tetrameric structure of hHMGR (PDB 1HWK).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4500850

substance\,\, pdbo{:}link\_to\_pdb \,\,pdbr{:}1HWK.}

If the Protein Data Bank (PDB) cross reference for the given MMDB record is provided, a link between the PubChem substance and the PDB record is exposed: If a PubChem substance was deposited by ChEMBL, it is cross-linked to EBI RDF [ 21 ] and ChEMBL RDF [ 27 ]: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\tt{substance{:}SID822166\,\,pdbo{:}link\_to\_pdb\,\,pdbr{:}1HWK.}

For instance, the pharmacological roles defined in ChEBI ontology can be used to annotate a given chemical found in PDB crystal structure [PDB:1HWK]: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\begin{aligned} &\tt{PREFIX\,\, obov{:} <http{:}//purl.obolibrary.org/obo\#>} \\ &\tt{SELECT\,\, DISTINCT\,\, ?

Publication Year: 2015