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 | adenosine diphosphate | Ligand Info | |||
| Canonical SMILES | C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N | ||||
| InChI | 1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 | ||||
| InChIKey | XTWYTFMLZFPYCI-KQYNXXCUSA-N | ||||
| PubChem Compound ID | 6022 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 4PRX E. coli GyrB 43-kDa N-terminal fragment in complex with ADP+Pi | ||||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [1] |
| PDB Sequence |
SYDSSSIKVL
13 KGLDAVRKRP23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI 63 HADNSVSVQD73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHAGGK103 FDDNSYKVSG 113 GLHGVGVSVV123 NALSQKLELV133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT 163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE 213 DHFHYEGGIK223 AFVEYLNKNK233 TPIHPNIFYF243 STEKDGIGVE253 VALQWNDGFQ 263 ENIYCFTNNI273 PQRDGGTHLA283 GFRAAMTRTL293 NAYMDKEGYS303 AREGLIAVVS 324 VKVPDPKFSS334 QTKDKLVSSE344 VKSAVEQQMN354 ELLAEYLLEN364 PTDAKIVVGK 374 IID
|
|||||
|
|
VAL43
4.474
ASN46
1.981
ALA47
3.277
ASP49
4.802
GLU50
2.882
ASP73
1.846
GLY75
4.983
ARG76
3.552
GLY77
3.348
ILE78
2.678
PRO79
3.385
ILE94
2.391
ALA100
2.884
GLY101
2.172
GLY102
1.998
|
|||||
| PDB ID: 4PRV E. coli GyrB 43-kDa N-terminal fragment in complex with ADP | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
YDSSSIKVLK
14 GLDAVRKRPG24 MYIGDTDDGT34 GLHHMVFEVV44 DNAIDEALAG54 HCKEIIVTIH 64 ADNSVSVQDD74 GRGIPTGIHP84 EEGVSAAEVI94 MTVLHAGGKF104 DDNSYKVSGG 114 LHGVGVSVVN124 ALSQKLELVI134 QREGKIHRQI144 YEHGVPQAPL154 AVTGETEKTG 164 TMVRFWPSLE174 TFTNVTEFEY184 EILAKRLREL194 SFLNSGVSIR204 LRDKRDGKED 214 HFHYEGGIKA224 FVEYLNKNKT234 PIHPNIFYFS244 TEKDGIGVEV254 ALQWNDGFQE 264 NIYCFTNNIP274 QRDGGTHLAG284 FRAAMTRTLN294 AYMDKEGYRE317 GLIAVVSVKV 327 PDPKFSSQTK337 DKLVSSEVKS347 AVEQQMNELL357 AEYLLENPTD367 AKIVVGKIID 377 AARAREAAR
|
|||||
|
|
ASN46
3.077
ALA47
4.133
ASP49
4.748
GLU50
3.227
ASP73
2.896
GLY77
3.806
ILE78
3.282
PRO79
4.763
ILE94
3.206
ALA100
3.334
GLY101
3.570
GLY102
2.850
|
|||||
| PDB ID: 4PU9 E. coli GyrB 43-kDa N-terminal fragment in complex with ADP-BeF3 | ||||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [1] |
| PDB Sequence |
SYDSSSIKVL
13 KGLDAVRKRP23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI 63 HADNSVSVQD73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHAGGK103 FDDNSYKVSG 113 GLHGVGVSVV123 NALSQKLELV133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT 163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE 213 DHFHYEGGIK223 AFVEYLNKNK233 TPIHPNIFYF243 STEKDGIGVE253 VALQWNDGFQ 263 ENIYCFTNNI273 PQRDGGTHLA283 GFRAAMTRTL293 NAYMDKEGYS303 KREGLIAVVS 324 VKVPDPKFSS334 QTKDKLVSSE344 VKSAVEQQMN354 ELLAEYLLEN364 PTDAKIVVGK 374 IIDAARAREA384 ARRA
|
|||||
|
|
ASN46
2.776
ALA47
4.184
ASP49
4.795
GLU50
3.250
ASP73
2.767
GLY77
4.112
ILE78
3.306
PRO79
4.931
ILE94
3.455
ALA100
3.329
GLY101
3.719
GLY102
3.349
|
|||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structure of the N-terminal Gyrase B fragment in complex with ADP?Pi reveals rigid-body motion induced by ATP hydrolysis. PLoS One. 2014 Sep 9;9(9):e107289. | ||||
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