Primary Citation PubMed: 18230722
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Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.
(2010) Viruses 2
PubMed: 20376302 | PubMedCentral: PMC2850067 | DOI: 10.3390/v2020606
This figure also shows that the loss of interaction due to Y181C mutation is compensated by the interaction between cyanovinyl group and conserved Y183 (based on structures from pdb codes: 1dlo, 2zd1 ... nd 3bgr).
Publication Year: 2010
An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1.
(2010) Virol J 7
PubMed: 21172023 | PubMedCentral: PMC3022682 | DOI: 10.1186/1743-422X-7-369
(a) RT crystallographic structure 2ZD1 (1.8 Å) highlights the residues within the selected regions, Dark gray = p66 subunit, light gray = p55, dark blue = active site residues involved in dNTP... binding (K65, R72, D110, V111, G112, D113, A114, Y115, Q151), green = active site residues involved in DNA binding (L74, V75, D76, R78, N81, E89, Q91, L92, I94, G152, K154, P157, M230, G231), purple = active site residues with no specific annotations (W24, P25, F61), pink = YMDD motif (Y183, M184, D185, D186), and light blue = residues involved in NNRTI binding (L100, K101, K102, K103, V179, Y188, G190, F227; not conserved).
Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development.
(2011) PLoS One 6
PubMed: 22132107 | PubMedCentral: PMC3223189 | DOI: 10.1371/journal.pone.0027518
PDB X-ray structure 2ZD1 of RT with Rilpivirine, an NNRTI like the analog series we modeled and shown in grey.
The residues used to define the binding site are shown in Figure 2 (PDB Code 2ZD1, HIV RT bound to Rilpivirine  , created with Molsoft ICM version 3.6-h) and Table 1 .
Publication Year: 2011
A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants.
(2012) Retrovirology 9
PubMed: 23217210 | PubMedCentral: PMC3549755 | DOI: 10.1186/1742-4690-9-99
The model of 1 bound to Y188L RT was based on the previously reported crystal structure of the WT RT/ 1 complex (PDB ID: 2ZD1 [ 11 ]).
Publication Year: 2012
Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase.
(2013) Nat Chem 5
PubMed: 23422558 | PubMedCentral: PMC3607437 | DOI: 10.1038/nchem.1559
The X-ray crystal structures of rilpivirine bound to the hydrophobic pocket of wild-type and two double mutant RTs (PDB: 2ZD1, 2ZE2, 3BGR), including crystallographic water, was solvated in a truncate... octahedral periodic container, with a minimum distance of 8 Å between any protein or drug atom and the closest container edge.
Publication Year: 2013
Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition.
(2014) PeerJ 2
PubMed: 25071993 | PubMedCentral: PMC4103094 | DOI: 10.7717/peerj.470
Computational Methods All computations were performed in YASARA ( Krieger et al., 2004 ) using the crystal structure of the rilpivirine-inhibited HIV1 reverse transcriptase published by Das et al. (PD... : 2ZD1) ( Das et al., 2008 ).
Publication Year: 2014
Differential binding of tenofovir and adefovir to reverse transcriptase of hepatitis B virus.
(2014) PLoS One 9
PubMed: 25180507 | PubMedCentral: PMC4152281 | DOI: 10.1371/journal.pone.0106324
In short, wt and mutant HBV RT sequences were submitted to i -TASSER  for combined homology/ab initio 3D-modeling with HIV-1 RT (PDB id 1JLE) as custom-supplied template structure in addition to P... B structures selected by i -TASSER for HBV RT modeling (i.e: 1M8X, RNA binding domain of human Puf protein; 1RW3, MMLV RT; 2ZD1 and 1VRT, both HIV-1 RT).
Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors.
(2014) Viruses 6
PubMed: 25254383 | PubMedCentral: PMC4189038 | DOI: 10.3390/v6093535
The RT backbone (PDB file 2ZD1) [ 30 ] is shown in ribbon representation (p66 in light gray and p51 in magenta).
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