Citations in PubMed

Primary Citation PubMed: 7540934 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.

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Specific binding of a hexanucleotide to HIV-1 reverse transcriptase: a novel class of bioactive molecules.

(2006) Nucleic Acids Res 34

PubMed: 17038335 | PubMedCentral: PMC1635251 | DOI: 10.1093/nar/gkl533

Modeling and docking studies Rigid-body docking studies of HIV-1 RT (Brookhaven Protein Data Bank accession nos: 1HMV, 1RTH, 1RTD and 1HVU) and Hex-S3 were performed with the program Hex 4.2 ( 15 ).

Publication Year: 2006


The y271 and i274 amino acids in reverse transcriptase of human immunodeficiency virus-1 are critical to protein stability.

(2009) PLoS One 4

PubMed: 19578544 | PubMedCentral: PMC2701634 | DOI: 10.1371/journal.pone.0006108

Based on the X-ray crystal structures of HIV-1 RT (1RTH) from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), structural models of wild type and mutant RTs were ... nalyzed using Swiss-PdbViewer software ( http://spdbv.vital-it.ch/ ).

(A) Locations of residues 271 and 274 in HIV-1 RT subunits p66 (grey) and p51 (green) (PDB coordinate 1RTH).

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


Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors.

(2012) Biology (Basel) 1

PubMed: 24832224 | PubMedCentral: PMC4009785 | DOI: 10.3390/biology1020222

This was based on analysis of the 1RTH NVP bound and 1FK9 EFV bound PDB crystal structures.

Influence of Initial Crystal Structure Choice If the differences observed between the modes seen for 1FK9 and 1RTH is caused by differences in the bound inhibitor, then similar differences should be observed using different EFV and NVP bound structures.

Figure 6 Comparison of the first 15 ANM modes generated from different HIV-1 RT structures bound to NVP and EFV, using the 1RTH and 1VRT NVP bound structures and 1FK9 and 1IKW EFV bound structures.

Figure 4 The fluctuations of the NNRTI bound HIV-1 RT described by the second ANM mode for ( a ) the EFV bound 1FK9 and ( b ) NVP bound 1RTH structures.

In ( c ) the 1IKW (EFV) and 1VRT (NVP) bound structures are compared, more of the low modes show high levels of similarity than in the plot for 1FK9 and 1RTH shown in Figure 2 c. Figure 7 Comparison of the squared fluctuations predicted by ANM mode 2 of the NVP bound 1VRT (red) and EFV bound 1IKW structures (black).

Figure 3 Comparison of the first 15 ANM modes generated from the apo HIV-1 RT structure and those of the NVP and EFV bound enzyme using the 1DLO, 1RTH and 1FK9 crystal structures respectively.

Figure 5 Comparison of the squared fluctuations predicted by ANM mode 2 of the NVP bound 1RTH (red) and EFV bound 1FK9 structures (black).

Publication Year: 2012


Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.

(2014) Nucleic Acids Res 42

PubMed: 24880687 | PubMedCentral: PMC4081091 | DOI: 10.1093/nar/gku487

Differences in subdomain arrangements are also observed from comparison of multiple crystal structures of RT/NVP binary complex; e.g. PDB IDs 3HVT ( 34 ) versus 1RTH ( 51 ).

Publication Year: 2014


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