The small-molecule RNAP inhibitors of Escherichia coli：
The structures of all RNA polymerases are superimposed, and the pockets where the inhibitors bind intensively are found and numbered pocket 1, pocket 2, pocket 3, etc. A table of inhibitors in each pocket, including inhibitor name, drug name, 2D structure, and 3D visualization.The ID and PDB are linked to PDB database.
| ID | PDB | Name | Drug | 2D Diagram | 3D Interaction | |
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| Pocket1 | 42S | 4XSX | N'-hydroxy-N-phenyl-3-(trifluoromethyl)benzenecarboximidamide |
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| 42T | 4XSY | 3-{[(2,6-dichlorophenyl)carbamoyl]amino}-N-hydroxy-N'-phenyl-5-(trifluoromethyl)benzenecarboximidamide |
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| 42U | 4XSZ | 4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline |
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| 4OB | 4ZH2 | N-hydroxy-N'-phenyl-3-(trifluoromethyl)benzenecarboximidamide |
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| 4OD | 4ZH3 | N'-(3-bromophenyl)-4-fluoro-N-hydroxy-3-(trifluoromethyl)benzenecarboximidamide |
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| 4OE | 4ZH4 | 5-(4-fluorophenyl)-4-[4-fluoro-3-(trifluoromethyl)phenyl]-1H-pyrazole |
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| Pocket2 | 1RL | 4KN4 | [(7S,9E,12R,13S,14R,15R,16R,17S,18S,19E,21E)-32-[2-(diethylamino)ethoxy]-15,17,37-trihydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-2,6,23-trioxo-8,27,38-trioxa-24,34-diazahexacyclo[23.11.1.14,7.05,36.026,35.028,33]octatriaconta-1(37),3,5(36),9,19,21,25,28(33),29,31,34-undecaen-13-yl] acetate | Benzoxazinorifamycin-2b |
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| 1RM | 4KN7 | [(7S,9E,11S,12R,13S,14R,15R,16R,17S,18S,19E,21E)-15,17,37-trihydroxy-32-[4-[4-(2-imidazol-1-ylethyl)piperazin-1-yl]butoxy]-11-methoxy-3,7,12,14,16,18,22-heptamethyl-2,6,23-trioxo-8,27,38-trioxa-24,34-diazahexacyclo[23.11.1.14,7.05,36.026,35.028,33]octatriaconta-1(37),3,5(36),9,19,21,25,28(33),29,31,34-undecaen-13-yl] acetate | Benzoxazinorifamycin-2c |
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| KNG | 6CUX | 4-[1-[(9E,19E,21E)-13-acetyloxy-2,15,17-trihydroxy-3,7,12,14,16,22-hexamethyl-11-[(4-methyl-4,6,7,7a-tetrahydro-3aH-[1,3]dioxolo[4,5-c]pyran-6-yl)oxy]-6,23,27,29-tetraoxo-8,30-dioxa-24-azatetracyclo[23.3.1.14,7.05,28]triaconta-1(28),2,4,9,19,21,25-heptaen-18-yl]ethoxy]-3,3-dimethyl-4-oxobutanoic acid | Kanglemycin A |
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| RFP | 4KMU | [(7S,9E,11S,12R,13S,14R,15R,16R,17S,18S,19E,21Z)-2,15,17,27,29-pentahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-26-[(E)-(4-methylpiperazin-1-yl)iminomethyl]-6,23-dioxo-8,30-dioxa-24-azatetracyclo[23.3.1.14,7.05,28]triaconta-1(29),2,4,9,19,21,25,27-octaen-13-yl] acetate | RIFAMPICIN |
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| 5UAC | ||||||
| 5UAH | ||||||
| 5UAL | ||||||
| Pocket3 | 4C2 | 4YFN | N-[3,4-Dioxo-2-(4-{[4-(Trifluoromethyl)benzyl]amino}piperidin-1-Yl)cyclobut-1-En-1-Yl]-3,5-Dimethyl-1,2-Oxazole-4-Sulfonamide |
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| 4C4 | 4YFX | methyl N-[(E,5R)-5-[5-[(2E,4E)-2,5-dimethylnona-2,4-dienoyl]-4-hydroxy-6-oxopyran-2-yl]hex-1-enyl]carbamate | Myxopyronin B |
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| 4C6 | 4YFK | 3,5-dimethyl-N-[2-[4-[(4-methylphenyl)methyl]piperidin-1-yl]-3,4-dioxocyclobuten-1-yl]-1,2-oxazole-4-sulfonamide |
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| QZY | 6VJS | 3-[[benzyl(ethyl)carbamoyl]amino]-5-(4-phenoxyphenyl)thiophene-2-carboxylic acid |
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