Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T25136 | Target Info | |||
| Target Name | Human immunodeficiency virus Ribonuclease H (HIV RNH) | ||||
| Synonyms | Retroviral ribonuclease H; RNase H (600-1159); RNH1 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | HIV RNH | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: 2'-deoxythymidine triphosphate | Ligand Info | |||||
| Structure Description | STRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: IMPLICATIONS FOR NUCLEOSIDE ANALOG DRUG RESISTANCE | PDB:1RTD | ||||
| Method | X-ray diffraction | Resolution | 3.20 Å | Mutation | Yes | [1] |
| PDB Sequence |
KISPIETVPV
10 KLKPGMDGPK20 VKQWPLTEEK30 IKALVEICTE40 MEKEGKISKI50 GPENPYNTPV 60 FAIKKKDSTK70 WRKLVDFREL80 NKRTQDFWEV90 QLGIPHPAGL100 KKKKSVTVLD 110 VGDAYFSVPL120 DEDFRKYTAF130 TIPSINNETP140 GIRYQYNVLP150 QGWKGSPAIF 160 QSSMTKILEP170 FRKQNPDIVI180 YQYMDDLYVG190 SDLEIGQHRT200 KIEELRQHLL 210 RWGLTTPDKK220 HQKEPPFLWM230 GYELHPDKWT240 VQPIVLPEKD250 SWTVNDICKL 260 VGKLNWASQI270 YPGIKVRQLC280 KLLRGTKALT290 EVIPLTEEAE300 LELAENREIL 310 KEPVHGVYYD320 PSKDLIAEIQ330 KQGQGQWTYQ340 IYQEPFKNLK350 TGKYARMRGA 360 HTNDVKQLTE370 AVQKITTESI380 VIWGKTPKFK390 LPIQKETWET400 WWTEYWQATW 410 IPEWEFVNTP420 PLVKLWYQLE430 KEPIVGAETF440 YVDGAANRET450 KLGKAGYVTN 460 KGRQKVVPLT470 DTTNQKTQLQ480 AIYLALQDSG490 LEVNIVTDSQ500 YALGIIQAQP 510 DESESELVNQ520 IIEQLIKKEK530 VYLAWVPAHK540 GIGGNEQVDK550 LVSA |
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| Ligand Name: (2-Acetyl-5-methylanilino)(2,6-dibromophenyl)acetamide | Ligand Info | |||||
| Structure Description | STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN A COMPLEX WITH THE NONNUCLEOSIDE INHIBITOR ALPHA-APA R 95845 AT 2.8 ANGSTROMS RESOLUTION | PDB:1HNI | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [2] |
| PDB Sequence |
PISPIETVPV
10 KLKPGMDGPK20 VKQWPLTEEK30 IKALVEICTE40 MEKEGKISKI50 GPENPYNTPV 60 FAIKKKDSTK70 WRKLVDFREL80 NKRTQDFWEV90 QLGIPHPAGL100 KKKKSVTVLD 110 VGDAYFSVPL120 DEDFRKYTAF130 TIPSINNETP140 GIRYQYNVLP150 QGWKGSPAIF 160 QSSMTKILEP170 FKKQNPDIVI180 YQYMDDLYVG190 SDLEIGQHRT200 KIEELRQHLL 210 RWGLTTPDKK220 HQKEPPFLWM230 GYELHPDKWT240 VQPIVLPEKD250 SWTVNDIQKL 260 VGKLNWASQI270 YPGIKVRQLS280 KLLRGTKALT290 EVIPLTEEAE300 LELAENREIL 310 KEPVHGVYYD320 PSKDLIAEIQ330 KQGQGQWTYQ340 IYQEPFKNLK350 TGKYARMRGA 360 HTNDVKQLTE370 AVQKITTESI380 VIWGKTPKFK390 LPIQKETWET400 WWTEYWQATW 410 IPEWEFVNTP420 PLVKLWYQLE430 KEPIVGAETF440 YVDGAANRET450 KLGKAGYVTN 460 KGRQKVVPLT470 NTTNQKTELQ480 AIYLALQDSG490 LEVNIVTDSQ500 YALGIIQAQP 510 DKSESELVNQ520 IIEQLIKKEK530 VYLAWVPAHK540 GIGGNEQVDK550 LVSAGIRK |
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| Ligand Name: 2',3'-Dideoxy-guanosine-5'-monophosphate | Ligand Info | |||||
| Structure Description | HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate | PDB:1T05 | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | Yes | [3] |
| PDB Sequence |
PISPIETVPV
10 KLKPGMDGPK20 VKQWPLTEEK30 IKALVEICTE40 MEKEGKISKI50 GPENPYNTPV 60 FAIKKKDSTK70 WRKLVDFREL80 NKRTQDFWEV90 QLGIPHPAGL100 KKKKSVTVLD 110 VGDAYFSVPL120 DEDFRKYTAF130 TIPSINNETP140 GIRYQYNVLP150 QGWKGSPAIF 160 QSSMTKILEP170 FKKQNPDIVI180 YQYMDDLYVG190 SDLEIGQHRT200 KIEELRQHLL 210 RWGLTTPDKK220 HQKEPPFLWM230 GYELHPDKWT240 VQPIVLPEKD250 SWTVNDICKL 260 VGKLNWASQI270 YPGIKVRQLS280 KLLRGTKALT290 EVIPLTEEAE300 LELAENREIL 310 KEPVHGVYYD320 PSKDLIAEIQ330 KQGQGQWTYQ340 IYQEPFKNLK350 TGKYARMRGA 360 HTNDVKQLTE370 AVQKITTESI380 VIWGKTPKFK390 LPIQKETWET400 WWTEYWQATW 410 IPEWEFVNTP420 PLVKLWYQLE430 KEPIVGAETF440 YVDGAANRET450 KLGKAGYVTN 460 KGRQKVVPLT470 NTTNQKTELQ480 AIYLALQDSG490 LEVNIVTDSQ500 YALGIIQAQP 510 DKSESELVNQ520 IIEQLIKKEK530 VYLAWVPAHK540 GIGGNEQVDK550 LVSA |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DDG or .DDG2 or .DDG3 or :3DDG;style chemicals stick;color identity;select .A:66 or .A:110 or .A:115 or .A:157 or .A:183 or .A:184 or .A:185 or .A:186 or .A:230 or .A:231; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N2-(3-Mercaptopropyl)-2'-deoxyguanosine-5'-monophosphate | Ligand Info | |||||
| Structure Description | HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate | PDB:1T05 | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | Yes | [3] |
| PDB Sequence |
PISPIETVPV
10 KLKPGMDGPK20 VKQWPLTEEK30 IKALVEICTE40 MEKEGKISKI50 GPENPYNTPV 60 FAIKKKDSTK70 WRKLVDFREL80 NKRTQDFWEV90 QLGIPHPAGL100 KKKKSVTVLD 110 VGDAYFSVPL120 DEDFRKYTAF130 TIPSINNETP140 GIRYQYNVLP150 QGWKGSPAIF 160 QSSMTKILEP170 FKKQNPDIVI180 YQYMDDLYVG190 SDLEIGQHRT200 KIEELRQHLL 210 RWGLTTPDKK220 HQKEPPFLWM230 GYELHPDKWT240 VQPIVLPEKD250 SWTVNDICKL 260 VGKLNWASQI270 YPGIKVRQLS280 KLLRGTKALT290 EVIPLTEEAE300 LELAENREIL 310 KEPVHGVYYD320 PSKDLIAEIQ330 KQGQGQWTYQ340 IYQEPFKNLK350 TGKYARMRGA 360 HTNDVKQLTE370 AVQKITTESI380 VIWGKTPKFK390 LPIQKETWET400 WWTEYWQATW 410 IPEWEFVNTP420 PLVKLWYQLE430 KEPIVGAETF440 YVDGAANRET450 KLGKAGYVTN 460 KGRQKVVPLT470 NTTNQKTELQ480 AIYLALQDSG490 LEVNIVTDSQ500 YALGIIQAQP 510 DKSESELVNQ520 IIEQLIKKEK530 VYLAWVPAHK540 GIGGNEQVDK550 LVSA |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MRG or .MRG2 or .MRG3 or :3MRG;style chemicals stick;color identity;select .A:258 or .A:289; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: [2-(6-Amino-9H-purin-9-YL)-1-methylethoxy]methyl-triphosphate | Ligand Info | |||||
| Structure Description | HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate | PDB:1T05 | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | Yes | [3] |
| PDB Sequence |
PISPIETVPV
10 KLKPGMDGPK20 VKQWPLTEEK30 IKALVEICTE40 MEKEGKISKI50 GPENPYNTPV 60 FAIKKKDSTK70 WRKLVDFREL80 NKRTQDFWEV90 QLGIPHPAGL100 KKKKSVTVLD 110 VGDAYFSVPL120 DEDFRKYTAF130 TIPSINNETP140 GIRYQYNVLP150 QGWKGSPAIF 160 QSSMTKILEP170 FKKQNPDIVI180 YQYMDDLYVG190 SDLEIGQHRT200 KIEELRQHLL 210 RWGLTTPDKK220 HQKEPPFLWM230 GYELHPDKWT240 VQPIVLPEKD250 SWTVNDICKL 260 VGKLNWASQI270 YPGIKVRQLS280 KLLRGTKALT290 EVIPLTEEAE300 LELAENREIL 310 KEPVHGVYYD320 PSKDLIAEIQ330 KQGQGQWTYQ340 IYQEPFKNLK350 TGKYARMRGA 360 HTNDVKQLTE370 AVQKITTESI380 VIWGKTPKFK390 LPIQKETWET400 WWTEYWQATW 410 IPEWEFVNTP420 PLVKLWYQLE430 KEPIVGAETF440 YVDGAANRET450 KLGKAGYVTN 460 KGRQKVVPLT470 NTTNQKTELQ480 AIYLALQDSG490 LEVNIVTDSQ500 YALGIIQAQP 510 DKSESELVNQ520 IIEQLIKKEK530 VYLAWVPAHK540 GIGGNEQVDK550 LVSA |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TNV or .TNV2 or .TNV3 or :3TNV;style chemicals stick;color identity;select .A:63 or .A:65 or .A:72 or .A:74 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:115 or .A:151 or .A:152 or .A:184 or .A:185 or .A:219; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2,3-Dihydroxy-5-isopropylcyclohepta-2,4,6-trienone | Ligand Info | |||||
| Structure Description | HIV-1 Reverse Transcriptase Isolated RnaseH Domain with the Inhibitor beta-thujaplicinol Bound at the Active Site | PDB:3K2P | ||||
| Method | X-ray diffraction | Resolution | 2.04 Å | Mutation | No | [4] |
| PDB Sequence |
YQLEKEPIVG
436 AETFYVDGAA446 NRETKLGKAG456 YVTNKGRQKV466 VPLTNTTNQK476 TELQAIYLAL 486 QDSGLEVNIV496 TDSQYALGII506 QAQPDKSESE516 LVNQIIEQLI526 KKEKVYLAWV 536 PAHKGIGGNE546 QVDKLVSAGI556 R
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JTH or .JTH2 or .JTH3 or :3JTH;style chemicals stick;color identity;select .A:443 or .A:444 or .A:474 or .A:478 or .A:498 or .A:538 or .A:539 or .A:549 or .A:557; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (7,8-Dihydroxy-2-Oxo-2h-Chromen-4-Yl)acetic Acid | Ligand Info | |||||
| Structure Description | Structure of a dihydroxycoumarin active-site inhibitor in complex with the RNASE H domain of HIV-1 reverse transcriptase | PDB:4QAG | ||||
| Method | X-ray diffraction | Resolution | 1.71 Å | Mutation | No | [5] |
| PDB Sequence |
LWYQLEKEPI
434 VGAETFYVDG444 AANRETKLGK454 AGYVTNKGRQ464 KVVPLTNTTN474 QKTELQAIYL 484 ALQDSGLEVN494 IVTDSQYALG504 IIQAQPDKSE514 SELVNQIIEQ524 LIKKEKVYLA 534 WVPAHKGIGG544 NEQVDKLVSA554 GIR
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .F95 or .F952 or .F953 or :3F95;style chemicals stick;color identity;select .A:443 or .A:444 or .A:478 or .A:498 or .A:499 or .A:500 or .A:538 or .A:539 or .A:549; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science. 1998 Nov 27;282(5394):1669-75. | ||||
| REF 2 | Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 A resolution. Structure. 1995 Apr 15;3(4):365-79. | ||||
| REF 3 | Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir. Nat Struct Mol Biol. 2004 May;11(5):469-74. | ||||
| REF 4 | Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site. Structure. 2009 Dec 9;17(12):1625-1635. | ||||
| REF 5 | Structure of a dihydroxycoumarin active-site inhibitor in complex with the RNase H domain of HIV-1 reverse transcriptase and structure-activity analysis of inhibitor analogs. J Mol Biol. 2014 Jul 15;426(14):2617-31. | ||||
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