The small-molecule RNAP inhibitors of Thermus thermophilus：
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 | |
|---|---|---|---|---|---|---|
| Pocket1 | TGT | 2BE5 | (1R,4R,5R,6R,7S,8R)-6-acetyloxy-7-amino-4-carbamoyl-4-hydroxy-8-phosphonooxy-9-oxa-3-thiabicyclo[3.3.1]nonane-1-carboxylic acid | Tagetitoxin |
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| Pocket2 | PUM | 5X21 | (1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl-N~2~-hydroxy-L-glutaminyl)amino]-5-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol | Pseudouridimycin |
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| Pocket3 | STD | 2PPB | (2S)-2-[(2S)-4-[(2E,4E,6R)-6-[(1R,3R,4S,5R,8R)-1,4-dimethylspiro[2,9-dioxabicyclo[3.3.1]non-6-ene-8,2'-oxirane]-3-yl]-4-methylhepta-2,4-dienoyl]-1-[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]-3,5-dioxopyrrolidin-4-id-2-yl]-N-methylpropanamide | Streptolydigin |
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| 1ZYR | ||||||
| 2A6H | ||||||
| Pocket4 | KNG | 6CUU | 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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| RBT | 2A68 | [(7S,9E,11S,12R,13S,14R,15R,16R,17S,18S,19E,21Z)-2,15,17,32-tetrahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-1'-(2-methylpropyl)-6,23-dioxospiro[8,33-dioxa-24,27,29-triazapentacyclo[23.6.1.14,7.05,31.026,30]tritriaconta-1(32),2,4,9,19,21,24,26,30-nonaene-28,4'-piperidine]-13-yl] acetate | Rifabutin |
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| RFV | 4OIR | (2S)-2-[(1E,3S,4R,5S,6R,7R,8R,9S,10S,11E,13Z)-5-acetyloxy-15-amino-7,9-dihydroxy-3-methoxy-4,6,8,10,14-pentamethyl-15-oxopentadeca-1,11,13-trienoxy]-2,4-dimethyl-1,6,7-trioxobenzo[e][1]benzofuran-5,9-diolate | Rifamycin SV |
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| RPT | 2A69 | [(7S,9E,11S,12R,13S,14R,15R,16R,17S,18S,19E,21Z)-26-[(E)-(4-cyclopentylpiperazin-1-yl)iminomethyl]-2,15,17,27,29-pentahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-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 | Rifapentine |
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| Pocket5 | MXP | 3EQL | 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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| NE6 | 3DXJ | Methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate |
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