Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T02228 | Target Info | |||
| Target Name | Streptococcus Topoisomerase IV A (Stre-coc parC) | ||||
| Synonyms | parC of Streptococcus pneumoniae serotype 4; DNA topoisomerase IV of Streptococcus pneumoniae serotype 4 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | Stre-coc parC | ||||
| Biochemical Class | Topoisomerase GyrA ParC | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Levofloxacin | Ligand Info | |||||
| Structure Description | Detailed structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases | PDB:3K9F | ||||
| Method | X-ray diffraction | Resolution | 2.90 Å | Mutation | No | [1] |
| PDB Sequence |
NIQNMSLEDI
12 MGERFGRYSK22 YIIQDRALPD32 IRDGLKPVQR42 RILYSMNKDS52 NTFDKSYRKS 62 AKSVGNIMGN72 FHPHGDSSIY82 DAMVRMSQNW92 KNREILVEMH102 GNNGSMDGDP 112 PAAMRYTEAR122 LSEIAGYLLQ132 DIEKKTVPFA142 WNFDDTEKEP152 TVLPAAFPNL 162 LVNGSTGISA172 GYATDIPPHN182 LAEVIDAAVY192 MIDHPTAKID202 KLMEFLPGPD 212 FPTGAIIQGR222 DEIKKAYETG232 KGRVVVRSKT242 EIEKLKGGKE252 QIVITEIPYE 262 INKANLVKKI272 DDVRVNNKVA282 GIAEVRDESD292 RDGLRIAIEL302 KKDANTELVL 312 NYLFKYTDLQ322 INYNFNMVAI332 DNFTPRQVGI342 VPILSSYIAH352 RREVILARSR 362 FDKEKAEKRL372 HIVEGLIRVI382 SILDEVIALI392 RASENKADAK402 ENLKVSYDFT 412 EEQAEAIVTL422 QLYRLTNTDV432 VVLQEEEAEL442 REKIAMLAAI452 IGDERTMYNL 462 MKKELREVKK472 KFATPRLSSL482 E
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Trovafloxacin | Ligand Info | |||||
| Structure Description | Quinolone(Trovafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae | PDB:4KOE | ||||
| Method | X-ray diffraction | Resolution | 3.02 Å | Mutation | Yes | [2] |
| PDB Sequence |
NIQNMSLEDI
12 MGERFGRYSK22 YIIQDRALPD32 IRDGLKPVQR42 RILYSMNKDS52 NTFDKSYRKS 62 AKSVGNIMGN72 FHPHGDSSIY82 DAMVRMSQNW92 KNREILVEMH102 GNNGSMDGDP 112 PAAMRYTEAR122 LSEIAGYLLQ132 DIEKKTVPFA142 WNFDDTEKEP152 TVLPAAFPNL 162 LVNGSTGISA172 GYATDIPPHN182 LAEVIDAAVY192 MIDHPTAKID202 KLMEFLPGPD 212 FPTGAIIQGR222 DEIKKAYETG232 KGRVVVRSKT242 EIEKLKGGKE252 QIVITEIPYE 262 INKANLVKKI272 DDVRVNNKVA282 GIAEVRDESD292 RDGLRIAIEL302 KKDANTELVL 312 NYLFKYTDLQ322 INYNFNMVAI332 DNFTPRQVGI342 VPILSSYIAH352 RREVILARSR 362 FDKEKAEKRL372 HIVEGLIRVI382 SILDEVIALI392 RASENKADAK402 ENLKVSYDFT 412 EEQAEAIVTL422 QLYRLTNTDV432 VVLQEEEAEL442 REKIAMLAAI452 IGDERTMYNL 462 MKKELREVKK472 KFATPRLSSL482 ED
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| Ligand Name: Moxifloxacin | Ligand Info | |||||
| Structure Description | Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases | PDB:3FOF | ||||
| Method | X-ray diffraction | Resolution | 4.00 Å | Mutation | No | [3] |
| PDB Sequence |
QNMSLEDIMG
14 ERFGRYSKYI24 IQDRALPDIR34 DGLKPVQRRI44 LYSMNKDSND56 KSYRKSAKSV 66 GNIMGNFHPH76 GDSSIYDAMV86 RMSQNWKNRE96 ILVEMHGNNG106 SMDGDPPAAM 116 RYTEARLSEI126 AGYLLQDIEK136 KTVPFAWNFD146 DTEKEPTVLP156 AAFPNLLVNT 176 DIPPHNLAEV186 IDAAVYMIDH196 PTAKIDKLME206 FLPGPDFPTG216 AIIQGRDEIK 226 KAYETGGRVV237 VRSKTEIEKL247 KGGKEQIVIT257 EINKANLVKK271 IDDVRVNNKV 281 IELTELVLNY314 LFKYTDLQIN324 YNFNMVAIDN334 FTPRQVGIVP344 ILSSYIAHRR 354 EVILARSRFD364 KEKAEKRLHI374 VEGLIRVISI384 LDEVIALIRA394 SENKADAKEN 404 LKVSYDFTEE414 QAEAIVTLQL424 YRLTNTDVVV434 LQEEEAELRE444 KIAMLAAIIG 454 DERTMYNLMK464 KELREVKKKF474 ATPRL
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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 .MFX or .MFX2 or .MFX3 or :3MFX;style chemicals stick;color identity;select .A:77 or .A:78 or .A:79 or .A:80 or .A:81 or .A:83 or .A:118; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-Amino-7-{(3r)-3-[(1s)-1-Aminoethyl]pyrrolidin-1-Yl}-1-Cyclopropyl-6-Fluoro-8-Methylquinazoline-2,4(1h,3h)-Dione | Ligand Info | |||||
| Structure Description | Inhibitor-stabilized topoisomerase IV-DNA cleavage complex (S. pneumoniae) | PDB:3LTN | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [1] |
| PDB Sequence |
NIQNMSLEDI
12 MGERFGRYSK22 YIIQDRALPD32 IRDGLKPVQR42 RILYSMNKDS52 NTFDKSYRKS 62 AKSVGNIMGN72 FHPHGDSSIY82 DAMVRMSQNW92 KNREILVEMH102 GNNGSMDGDP 112 PAAMRYTEAR122 LSEIAGYLLQ132 DIEKKTVPFA142 WNFDDTEKEP152 TVLPAAFPNL 162 LVNGSTGISA172 GYATDIPPHN182 LAEVIDAAVY192 MIDHPTAKID202 KLMEFLPGPD 212 FPTGAIIQGR222 DEIKKAYETG232 KGRVVVRSKT242 EIEKLKGGKE252 QIVITEIPYE 262 INKANLVKKI272 DDVRVNNKVA282 GIAEVRDESD292 RDGLRIAIEL302 KKDANTELVL 312 NYLFKYTDLQ322 INYNFNMVAI332 DNFTPRQVGI342 VPILSSYIAH352 RREVILARSR 362 FDKEKAEKRL372 HIVEGLIRVI382 SILDEVIALI392 RASENKADAK402 ENLKVSYDFT 412 EEQAEAIVTL422 QLYRLTNTDV432 VVLQEEEAEL442 REKIAMLAAI452 IGDERTMYNL 462 MKKELREVKK472 KFATPRLSSL482 E
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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 .PDQ or .PDQ2 or .PDQ3 or :3PDQ;style chemicals stick;color identity;select .A:79 or .A:117 or .A:118; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (3as,4r)-4-Amino-13-Cyclopropyl-8-Fluoro-10-Oxo-3a,4,5,6,10,13-Hexahydro-1h,3h-Pyrrolo[2',1':3,4][1,4]oxazepino[5,6-H]quinoline-11-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate | PDB:4KPF | ||||
| Method | X-ray diffraction | Resolution | 3.24 Å | Mutation | No | [4] |
| PDB Sequence |
NIQNMSLEDI
12 MGERFGRYSK22 YIIQDRALPD32 IRDGLKPVQR42 RILYSMNKDS52 NTFDKSYRKS 62 AKSVGNIMGN72 FHPHGDSSIY82 DAMVRMSQNW92 KNREILVEMH102 GNNGSMDGDP 112 PAAMRYTEAR122 LSEIAGYLLQ132 DIEKKTVPFA142 WNFDDTEKEP152 TVLPAAFPNL 162 LVNGSTGISA172 GYATDIPPHN182 LAEVIDAAVY192 MIDHPTAKID202 KLMEFLPGPD 212 FPTGAIIQGR222 DEIKKAYETG232 KGRVVVRSKT242 EIEKLKGGKE252 QIVITEIPYE 262 INKANLVKKI272 DDVRVNNKVA282 GIAEVRDESD292 RDGLRIAIEL302 KKDANTELVL 312 NYLFKYTDLQ322 INYNFNMVAI332 DNFTPRQVGI342 VPILSSYIAH352 RREVILARSR 362 FDKEKAEKRL372 HIVEGLIRVI382 SILDEVIALI392 RASENKADAK402 ENLKVSYDFT 412 EEQAEAIVTL422 QLYRLTNTDV432 VVLQEEEAEL442 REKIAMLAAI452 IGDERTMYNL 462 MKKELREVKK472 KFATPRLSSL482 ED
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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 .1UV or .1UV2 or .1UV3 or :31UV;style chemicals stick;color identity;select .A:79 or .A:80 or .A:83 or .A:117 or .A:118; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 7-[(3R)-3-aminopyrrolidin-1-yl]-8-chloro-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid | Ligand Info | |||||
| Structure Description | Quinolone(Clinafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae | PDB:3RAD | ||||
| Method | X-ray diffraction | Resolution | 3.35 Å | Mutation | No | [4] |
| PDB Sequence |
NIQNMSLEDI
12 MGERFGRYSK22 YIIQDRALPD32 IRDGLKPVQR42 RILYSMNKDS52 NTFDKSYRKS 62 AKSVGNIMGN72 FHPHGDSSIY82 DAMVRMSQNW92 KNREILVEMH102 GNNGSMDGDP 112 PAAMRYTEAR122 LSEIAGYLLQ132 DIEKKTVPFA142 WNFDDTEKEP152 TVLPAAFPNL 162 LVNGSTGISA172 GYATDIPPHN182 LAEVIDAAVY192 MIDHPTAKID202 KLMEFLPGPD 212 FPTGAIIQGR222 DEIKKAYETG232 KGRVVVRSKT242 EIEKLKGGKE252 QIVITEIPYE 262 INKANLVKKI272 DDVRVNNKVA282 GIAEVRDESD292 RDGLRIAIEL302 KKDANTELVL 312 NYLFKYTDLQ322 INYNFNMVAI332 DNFTPRQVGI342 VPILSSYIAH352 RREVILARSR 362 FDKEKAEKRL372 HIVEGLIRVI382 SILDEVIALI392 RASENKADAK402 ENLKVSYDFT 412 EEQAEAIVTL422 QLYRLTNTDV432 VVLQEEEAEL442 REKIAMLAAI452 IGDERTMYNL 462 MKKELREVKK472 KFATPRLSSL482 ED
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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 .NFX or .NFX2 or .NFX3 or :3NFX;style chemicals stick;color identity;select .A:79 or .A:80 or .A:117 or .A:118; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (7ar,8r)-8-Amino-4-Cyclopropyl-12-Fluoro-1-Oxo-4,7,7a,8,9,10-Hexahydro-1h-Pyrrolo[1',2':1,7]azepino[2,3-H]quinoline-2-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate | PDB:4KPE | ||||
| Method | X-ray diffraction | Resolution | 3.43 Å | Mutation | Yes | [4] |
| PDB Sequence |
NIQNMSLEDI
12 MGERFGRYSK22 YIIQDRALPD32 IRDGLKPVQR42 RILYSMNKDS52 NTFDKSYRKS 62 AKSVGNIMGN72 FHPHGDSSIY82 DAMVRMSQNW92 KNREILVEMH102 GNNGSMDGDP 112 PAAMRYTEAR122 LSEIAGYLLQ132 DIEKKTVPFA142 WNFDDTEKEP152 TVLPAAFPNL 162 LVNGSTGISA172 GYATDIPPHN182 LAEVIDAAVY192 MIDHPTAKID202 KLMEFLPGPD 212 FPTGAIIQGR222 DEIKKAYETG232 KGRVVVRSKT242 EIEKLKGGKE252 QIVITEIPYE 262 INKANLVKKI272 DDVRVNNKVA282 GIAEVRDESD292 RDGLRIAIEL302 KKDANTELVL 312 NYLFKYTDLQ322 INYNFNMVAI332 DNFTPRQVGI342 VPILSSYIAH352 RREVILARSR 362 FDKEKAEKRL372 HIVEGLIRVI382 SILDEVIALI392 RASENKADAK402 ENLKVSYDFT 412 EEQAEAIVTL422 QLYRLTNTDV432 VVLQEEEAEL442 REKIAMLAAI452 IGDERTMYNL 462 MKKELREVKK472 KFATPRLSSL482 ED
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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 .AF5 or .AF52 or .AF53 or :3AF5;style chemicals stick;color identity;select .A:79 or .A:80 or .A:118; 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 | Structural basis of gate-DNA breakage and resealing by type II topoisomerases. PLoS One. 2010 Jun 28;5(6):e11338. | ||||
| REF 2 | Quinolone(Trovafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae | ||||
| REF 3 | Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nat Struct Mol Biol. 2009 Jun;16(6):667-9. | ||||
| REF 4 | Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones. Open Biol. 2016 Sep;6(9):160157. | ||||
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