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Document Table 1 Crystal Structures of HIV-1 Reverse Transcriptase PDB entry HIV-1 RT Structure Resolution Range (Å) R-Factor/Free R-Factor (%) Data Completeness (%) Page 46 Temperature (°C) References 1hmv unliganded RT 6.0-3.0 25.4/29.7 85 -165 41 1rtj unliganded RT 25.0-2.35 21.9 89.5 -173 42 1dlo unliganded RT 8.0-2.7 23.0/33.6 99.5 -165 43 1hmi RT/DNA/Fab 15.0-3.0 26.0 88.1 -10 38 3hvt RT/nevirapine 8.0-2.9 26.6 95.6 -165 31,32 1vrt RT/nevirapine 25.0-2.2 18.6 87.1 16 33 1rth RT/1051U91 25.0-2.2 21.4 81.4 16 33 1hni RT/α-APA (R95845) 10.0-2.8 25.5/36 78.5 -15 34 1vru RT/α-APA (R90385) 25.0-2.4 18.7 86.5 16 33 1hnv RT/8-Cl TIBO (R86183) 10.0-3.0 24.9/35.6 81 -10 35 1rev RT/9-Cl TIBO (R82913) 25.0-2.6 22.4 80.7 -173 36 1tvr RT/9-Cl TIBO (R82913) 10.0-3.0 25.9 72 -165 37 1rti RT/HEPT 25.0-3.0 23.6 86.3 14 33 1hrh RT (RNase H domain) 20.0-2.4 20.0 93.1 4 94 1rdh RT (RNase H domain) 20.0-2.8 21.5 95.6 4 95 1har RT (fingers and palm subdomains) 7.0-2.2 20.8/27.0 96 4 44 http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_46.html [4/5/2004 4:48:38 PM]
Document Figure 2 Ribbon diagrams of the three types of HIV-1 RT crystal structures. (a) Structure of the HIV-1 RT/DNA/Fab ternary complex [38]. The bound nucleic acid is shown as double-stranded helices with template strand in black and primer strand in gray. The Fab fragment is not shown. (b) Structure of the HIV-1 RT complexed with the NNRTI TIBO R86183 [34]. For the sake of clarity, the bound TIBO inhibitor is shown as an atomic model. (c) Structure of unliganded HIV-1 RT [41,43]. (d) A schematic diagram showing the resemblance of the HIV-1 RT p66 subunit to a human right hand. The RNase H domain, which has no counterpart for a human hand, is shown as an oval below the thumb. When a template-primer binds to HIV-1 RT, the fingers, palm, and thumb subdomains of p66 form a large cleft to bind the DNA. The polymerase active site (shown as a small circle) lies at the bottom of the DNA-binding cleft. The NNRTI binds in the highly hydrophobic NNIBP (shown as a large circle), which is located in the vicinity of the polymerase active site. The p66 thumb subdomain in the NNRTI-bound HIV-1 RT structures is in an upright position extended beyond that observed in the structure of RT with bound DNA. In the absence of any bound nucleic acid or NNRTI, however, the p66 thumb folds down into the DNA-binding cleft (shown as dashed drawing). http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_47.html [4/5/2004 4:48:52 PM] Page 47
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Structure-based Drug Design 14 Stru
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Document D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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