Primary Citation PubMed: 7540934
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A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites.
(2007) BMC Bioinformatics 8 Suppl 4
PubMed: 17570152 | PubMedCentral: PMC1892088 | DOI: 10.1186/1471-2105-8-S4-S9
(A) Immunoglobulin 48g7 germline fab (PDB id: 1AJ7 and 2RCS); (B) Adenylate kinase (PDB id: 1AKE and 4AKE); (C) HIV-1 reverse transcriptase (PDB id: 1VRT and 1RTJ); (D) Maltodextrin binding protein (P... B id: 1ANF and 1OMP).
Publication Year: 2007
HIV reverse transcriptase: structural interpretation of drug resistant genetic variants from India.
(2009) Bioinformation 4
PubMed: 20011151 | PubMedCentral: PMC2770369 | DOI: null
(D) RT structure that corresponds to open conformation (1RTJ, green) superposed on Efavirenz (in orange) bound RT (1IKW, yellow) (E) Interactions involving M230 in Nevirapine bound RT (1VRT) (F) Model... for M230L mutation.
(B-F) Local hydrogen bond interactions involving K101 in unliganded RT structure 1DLO,1HMV,1RTD, 1RTJ and in Nevirapine bound RT 1VRT (G) Structural superposition of 1IKW (yellow) and 1RTJ (green) showing changes in residue conformations.
The protein databank codes of the crystal structures of bound and unbound forms of RT used in this study are 1IKW [ 6 ], 1VRT [ 7 ], 1DLO [ 8 ], 1HMV [ 9 ], 1RTJ [ 10 ] and 1RTD [ 11 ].
(D)Changes due to K238T mutation (E) Comparison of side chain conformations of residues in the region involving Lys238, of Efavirenz bound RT, 1IKW (yellow) and of the unliganded form, 1RTJ (green) (F) Interactions involving K238 in Nevirapine bound RT (1VRT).
Publication Year: 2009
Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.
(2010) Viruses 2
PubMed: 20376302 | PubMedCentral: PMC2850067 | DOI: 10.3390/v2020606
Clockwise from top left: RT/Etravirine (PDB Code 1sv5), RT/nevirapine (1vrt), RT/delavirdine (1klm), and RT/efavirenz (1ikw).
Publication Year: 2010
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.
Predictive power of molecular dynamics receptor structures in virtual screening.
(2011) J Chem Inf Model 51
PubMed: 21534609 | PubMedCentral: PMC3124922 | DOI: 10.1021/ci200117n
( 39 ) The four different systems included two bound systems, 1VRT ( 40 ) structure with α-APA bound to NNIBP (α-APA bound) and 1VRT structure with UC-781 bound to NNIBP (UC-781 bound)... as well as two unbound systems, 1VRT structure with the NNRTI extracted from NNIBP (unbound open) and 1DLO structure( 41 ) (unbound closed).
Publication Year: 2011
HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
(2012) Nat Struct Mol Biol 19
PubMed: 22266819 | PubMedCentral: PMC3359132 | DOI: 10.1038/nsmb.2223
The thumb in the higher-resolution nevirapine-binary structure (PDB ID 1VRT) 21 is further extended ( Fig. 3a ) and involved in crystal contacts.
Publication Year: 2012
A polymorphism at position 400 in the connection subdomain of HIV-1 reverse transcriptase affects sensitivity to NNRTIs and RNaseH activity.
(2013) PLoS One 8
PubMed: 24098331 | PubMedCentral: PMC3788777 | DOI: 10.1371/journal.pone.0074078
The structures chosen contain HIV-1 RT bound to NVP (PDB: 1VRT), double stranded DNA (PDB: 2HMI), a hybrid RNA/DNA duplex based on the polypurine tract (PDB: 1HYS) and the apo enzyme (PDB: 1DLO).
Publication Year: 2013
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
Crystal structure projections are shown as black dots, except the 1IKW (green) and 1VRT (magenta) structures which were used as initial structures for the EFV and NVP MD simulations, respectively.
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.
These were the 1DLO apo structure, the 1IKW EFV bound structure and 1VRT NVP bound structure.
Two separate clusters of structures are apparent in this data, where we have labelled the two groups A and B. All structures in group A (including 1FK9,1IKW and 1VRT) show p51 flexibility in their second ANM modes, whereas those in group B do not.
Model Creation Unfortunately, all available HIV-1 RT crystal structures are incomplete and a number of loop residues in the p51 subunit of the NNRTI bound structures are missing (residues 217 to 231 in 1IKW, 88 to 92 and 215 to 231 in 1VRT, and 356 to 362 in both 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).
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  , and include all targets where at least two structures have an RMSD ave greater than 1.5 Å.
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).
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