Citations in PubMed

Primary Citation PubMed: 8648598 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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.

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Optimal assignment methods for ligand-based virtual screening.

(2009) J Cheminform 1

PubMed: 20150995 | PubMedCentral: PMC2820492 | DOI: 10.1186/1758-2946-1-14

target number actives number decoys number clusters a PDB code b ace c 46 1796 19 p 1o86 ache d 100 3859 18 1eve cdk2 e 47 2070 32 1ckp cox2 f 212 12606 44 1cx2 egfr g 365 15560 40 1m17 fxa h 64 2092 ... 9 1f0r hivrt i 34 1494 17 1rt1 inha j 57 2707 23 1p44 p38 k 137 6779 20 1kv2 pde5 l 26 1698 22 1xp0 pdgfrb m 124 5603 22 1t46 src n 98 5679 21 2src vegfr2 o 48 2712 31 1fgi Overview of the used data sets containing the number of actives, decoys, different chemotype clusters, and the PDB code of the complexed crystal structure which contains the search query.

Publication Year: 2009


Application of 3D Zernike descriptors to shape-based ligand similarity searching.

(2009) J Cheminform 1

PubMed: 20150998 | PubMedCentral: PMC2820497 | DOI: 10.1186/1758-2946-1-19

Target PDB Actives Decoys Decoys per active angiotensin-converting enzyme (ace) 1o86 46 1796 39.04 acetylcholinesterase (ache) 1eve 100 3859 38.59 cyclin-dependent kinase 2(cdk2) 1ckp 47 2070 44.04 cy... looxygenase-2(cox2) 1cx2 212 12606 59.46 epidermal growth factor receptor(egfr) 1m17 365 15560 42.63 factor Xa(fxa) 1f0r 64 2092 32.69 HIV reverse transcriptase(hivrt) 1rt1 34 1494 43.94 enoyl ACP reductase(inha) 1p44 57 2707 47.49 P38 mitogen activated protein(p38) 1kv2 137 6779 49.48 phosphodiesterase(pde5) 1xp0 26 1698 65.31 platelet derived growth factor receptor kinase(pdgfrb) 1t46 124 5603 45.19 tyrosine kinase SRC(src) 2src 98 5679 57.95 vascular endothelial growth factor receptor(vegfr2) 1fgi 48 2712 56.5 The third dataset from the National Cancer Institute (NCI) consists of 42,687 compounds derived from an assay measuring protection from HIV-1 infection of human CEM cells [ 57 ].

Publication Year: 2009


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


Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases.

(2013) Nucleic Acids Res 41

PubMed: 23275546 | PubMedCentral: PMC3561941 | DOI: 10.1093/nar/gks1251

Viral species and PDB structures used as queries in this study Queries Abbreviations PDB Length of structure Picornaviridae, RdRp, +ssRNA     Poliovirus PV 1RA6 ( 3 ) 4... 1     Poliovirus (open) PV 3OL6 ( 9 ) 471     Poliovirus (closed) PV 3OL7 ( 9 ) 471     Coxsackie virus COXV 3DDK ( 11 ) 462     Human rhinovirus HRV 1XR6 ( 12 ) 460     Human rhinovirus HRV 1XR7 ( 12 ) 460     Foot and mouth disease virus FMDV 1U09 ( 2 ) 476 Caliciviridae, RdRp, +ssRNA     Norwalk virus NV 1SH0 ( 13 ) 510     Rabbit hemorrhagic disease virus RHDV 1KHV ( 14 ) 516     Rabbit hemorrhagic disease virus RHDV 1KHW ( 14 ) 516     Sapporo virus SAPV 2CKW ( 15 ) 515 Flaviviridae, RdRp, +ssRNA     Hepatitis C virus HCV 1NB4 ( 16 ) 570     Hepatitis C virus HCV 1NB7 ( 16 ) 570     Bovine viral diarrhea virus BVDV 1S48 ( 17 ) 609     West Nile (Kunjin) virus WNV 2HCS ( 18 ) 595     Dengue virus DENV 2J7U ( 19 ) 635 Cystoviridae, RdRp, dsRNA     Bacteriophage Phi6 PHI6 1HHS ( 20 ) 664     Bacteriophage Phi6 PHI6 1HI0 ( 20 ) 664 Reoviridae, RdRp, dsRNA     Reovirus lambda 3 REOV 1MUK ( 21 ) 1267     Reovirus lambda 3 REOV 1N35 ( 21 ) 1267     Rotavirus ROTAV 2R7X ( 22 ) 1095 Birnaviridae, RdRp, dsRNA     Infectious bursal disease, birnavirus IBDV 2PGG ( 5 ) 774     Infectious pancreatic necrosis IPNV 2YI8 ( 23 ) 799     Infectious pancreatic necrosis IPNV 2YI9 ( 23 ) 799     Infectious pancreatic necrosis IPNV 2YIA ( 23 ) 799 RdDp     HIV1 HIV1 1RT1 ( 24 ) 560     HIV1 (closed) HIV1 1RTD ( 25 ) 554     HIV1 (open) HIV1 2HMI ( 26 ) 558     Tribolium castaneum TERT 3DU6 ( 27 ) 596 DdRp     Bacteriophage T7 (closed) T7 RNAP 1S77 ( 28 ) 883     Bacteriophage T7 (closed) T7 RNAP 2AJQ ( 29 ) 704     Bacteriophage T7 (open) T7 RNAP 1MSW ( 30 ) 883     Bacteriophage N4 N4 3C2P ( 31 ) 1117 DdDp     Thermus aquaticus (open) TAQ 2KTQ ( 32 ) 538     Thermus aquaticus (closed) TAQ 3KTQ ( 32 ) 540     Thermus aquaticus (open) TAQ 4KTQ ( 32 ) 539     Bacteriophage T7 T7 DNAP 1T7P ( 33 ) 698 Queries of both open and closed structures were used to assess the impact of this feature on R2R correspondence.

Publication Year: 2013


Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.

(2014) PLoS Comput Biol 10

PubMed: 25079060 | PubMedCentral: PMC4117425 | DOI: 10.1371/journal.pcbi.1003741

Target Structural data Docking-based druggability Protein flexibility Variation PDB ID RMSD ave (Å) [A] dock hit rate [B] DScore+ [A] [B] CDK2 1aq1 1.32 1.7 21% 11% 1buh 1.8 1.44 1.7 1dm2 1.8 ... .62 1.9 ER 1l2i 1.69 2.9 9% 7% 3ert 2.6 1.55 2.7 1err 2.0 1.61 2.8 HIV RT 1vrt 1.66 2.5 8% 13% 1rt1 1.5 1.75 2.3 1c1c 1.9 1.61 2.2 1rth 1.6 1.61 2.3 p38α 1a9u 1.00 1.8 49% 15% kinase 1kv1 3.8 1.16 2.1 1kv2 3.5 1.61 2.1 PPARγ 1fm6 1.46 2.9 13% 34% 1fm9 1.5 1.62 3.0 2prg 0.7 1.43 2.1 TK 1kim 1.58 2.7 12% 4% 1ki4 1.8 1.40 2.6 IL-2 1z92 0.13 * 107% 13% 1py2 2.6 0.62 * 1m48 2.5 0.62 * Bcl-XL 2bzw 1.04 2.4 21% 4% 2yxj 2.5 0.84 2.5 TNF 1tnf 0.95 2.4 1% 18% 2az5 2.9 0.96 2.0 MDM2 1ycr 0.45 2.5 69% 18% 1rv1 1.8 0.92 2.2 1t4e 1.6 0.66 2.1 HPV E2 1tue -0.24 * 323% 31% 1r6n 2.8 1.02 * Targets are from Huang and Jacobson [17] , and include all targets where at least two structures have an RMSD ave greater than 1.5 Å.

Publication Year: 2014