Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T81503 | Target Info | |||
| Target Name | Bacterial DNA gyrase B (Bact gyrB) | ||||
| Synonyms | gyrB; DNA gyrase subunit B | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | Bact gyrB | ||||
| Biochemical Class | ATP-hydrolyzing DNA topoisomerase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | 2-Aminobenzimidazole | Ligand Info | |||
| Canonical SMILES | C1=CC=C2C(=C1)NC(=N2)N | ||||
| InChI | 1S/C7H7N3/c8-7-9-5-3-1-2-4-6(5)10-7/h1-4H,(H3,8,9,10) | ||||
| InChIKey | JWYUFVNJZUSCSM-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 13624 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 5Z4O Bacterial GyrB ATPase domain in complex with a chemical fragment | ||||||
| Method | X-ray diffraction | Resolution | 1.73 Å | Mutation | No | [1] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLVGVSVVN124 ALSQKLELVI134 QREGKIHRQI 144 YEHGVPQAPL154 AVTGETEKTG164 TMVRFWPSLE174 TFTNVTEFEY184 EILAKRLREL 194 SFLNSGVSIR204 LRDKRDGKED214 HFHY
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| PDB ID: 5Z9F Bacterial GyrB ATPase domain in complex with a chemical fragment | ||||||
| Method | X-ray diffraction | Resolution | 1.76 Å | Mutation | No | [1] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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| PDB ID: 5Z9Q Bacterial GyrB ATPase domain in complex with a chemical fragment | ||||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [1] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDKEIIVT62 IHADNSVSVQ72 DDGRGIPTGI 82 HPEEGVSAAE92 VIMTVLGVGV120 SVVNALSQKL130 ELVIQREGKI140 HRQIYEHGVP 150 QAPLAVTGET160 EKTGTMVRFW170 PSLETFTNVT180 EFEYEILAKR190 LRELSFLNSG 200 VSIRLRDKRD210 GKEDHFHY
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| PDB ID: 5Z4H Bacterial GyrB ATPase domain in complex with a chemical fragment | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLHGVGVSV122 VNALSQKLEL132 VIQREGKIHR 142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF182 EYEILAKRLR 192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:147 or .A:149 or .A:174; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 5Z9B Bacterial GyrB ATPase domain in complex with (3,4-dichlorophenyl)hydrazine | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [1] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLHGVGVSV122 VNALSQKLEL132 VIQREGKIHR 142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF182 EYEILAKRLR 192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:147 or .A:149 or .A:174; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DPR E. coli GyrB ATPase domain in complex with methyl 3,4-dihydroxybenzoate | ||||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:146 or .A:147 or .A:149 or .A:174; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DQM E. coli GyrB ATPase domain in complex with Naringenin | ||||||
| Method | X-ray diffraction | Resolution | 1.78 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLDNSYKVS112 GGLHGVGVSV122 VNALSQKLEL 132 VIQREGKIHR142 QIYEHGVPQA152 PLAVTGETEK162 TGTMVRFWPS172 LETFTNVTEF 182 EYEILAKRLR192 ELSFLNSGVS202 IRLRDKRDGK212 EDHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:147 or .A:149 or .A:174; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DQF E. coli GyrB ATPase domain in complex with methyl 2,4-dihydroxybenzoate | ||||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:147 or .A:149 or .A:174; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DQS E. coli GyrB ATPase domain in complex with 2-chlorophenol | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLVGVSVVN124 ALSQKLELVI134 QREGKIHRQI 144 YEHGVPQAPL154 AVTGETEKTG164 TMVRFWPSLE174 TFTNVTEFEY184 EILAKRLREL 194 SFLNSGVSIR204 LRDKRDGKED214 HFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:146 or .A:147 or .A:149 or .A:174; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DQU E. coli GyrB ATPase domain in complex with methyl 4-hydroxybenzoate | ||||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:147 or .A:149 or .A:174; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DQW E. coli GyrB ATPase domain in complex with 4-chlorophenol | ||||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:147 or .A:149 or .A:174; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DOR E. coli GyrB ATPase domain in complex with 4-nitropheno | ||||||
| Method | X-ray diffraction | Resolution | 1.89 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:147 or .A:149 or .A:174; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DQH E. coli GyrB ATPase domain in complex with 2-hydroxybenzamide | ||||||
| Method | X-ray diffraction | Resolution | 1.91 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:147 or .A:149 or .A:174; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DQI E. coli GyrB ATPase domain in complex with Esculetin | ||||||
| Method | X-ray diffraction | Resolution | 1.91 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:146 or .A:147 or .A:149 or .A:174; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DQJ E. coli GyrB ATPase domain in complex with 3,4-Dihydroxyacetophenone | ||||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:146 or .A:147 or .A:149 or .A:174; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DQL E. coli GyrB ATPase domain in complex with 4-chlorobenzene-1,2-diol | ||||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:146 or .A:147 or .A:149 or .A:174; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7DPS E. coli GyrB ATPase domain in complex with Methyl 4-hydroxycinnamate | ||||||
| Method | X-ray diffraction | Resolution | 2.26 Å | Mutation | No | [2] |
| PDB Sequence |
LDAVRKRPGM
25 YIGDTDDGTG35 LHHMVFEVVD45 NAIDEALAGH55 CKEIIVTIHA65 DNSVSVQDDG 75 RGIPTGIHPE85 EGVSAAEVIM95 TVLGVGVSVV123 NALSQKLELV133 IQREGKIHRQ 143 IYEHGVPQAP153 LAVTGETEKT163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE 193 LSFLNSGVSI203 RLRDKRDGKE213 DHFHY
|
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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 .AX7 or .AX72 or .AX73 or :3AX7;style chemicals stick;color identity;select .A:20 or .A:146 or .A:147 or .A:149 or .A:174; 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 | Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes. Medchemcomm. 2018 Jul 4;9(10):1619-1629. | ||||
| REF 2 | Identification of new building blocks by fragment screening for discovering GyrB inhibitors. Bioorg Chem. 2021 Sep;114:105040. | ||||
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