Structure of PDB 7z9m Chain C Binding Site BS03

Receptor Information
>7z9m Chain C (length=517) Species: 511145 (Escherichia coli str. K-12 substr. MG1655) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGN
DWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQG
NFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPD
VMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEG
LMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRE
TIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEV
KRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRH
RREVVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAK
TALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQA
ILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELE
LVREQFGDKRRTEITAN
Ligand information
Ligand IDIL1
InChIInChI=1S/C42H35N11O9/c1-22(2)62-36-31(16-13-30(35(36)54)38(56)47-26-9-7-25(8-10-26)42(60)61)50-39(57)32-15-12-28(20-45-32)49-41(59)34(17-29-21-46-53-52-29)51-40(58)33-14-11-27(19-44-33)48-37(55)24-5-3-23(18-43)4-6-24/h3-16,19-22,34,54H,17H2,1-2H3,(H,47,56)(H,48,55)(H,49,59)(H,50,57)(H,51,58)(H,60,61)(H,46,52,53)/t34-/m0/s1
InChIKeyJOTLSOCKRKDRJG-UMSFTDKQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)Oc1c(ccc(c1O)C(=O)Nc2ccc(cc2)C(=O)O)NC(=O)c3ccc(cn3)NC(=O)[C@H](Cc4c[nH]nn4)NC(=O)c5ccc(cn5)NC(=O)c6ccc(cc6)C#N
CACTVS 3.385CC(C)Oc1c(O)c(ccc1NC(=O)c2ccc(NC(=O)[C@H](Cc3c[nH]nn3)NC(=O)c4ccc(NC(=O)c5ccc(cc5)C#N)cn4)cn2)C(=O)Nc6ccc(cc6)C(O)=O
OpenEye OEToolkits 2.0.7CC(C)Oc1c(ccc(c1O)C(=O)Nc2ccc(cc2)C(=O)O)NC(=O)c3ccc(cn3)NC(=O)C(Cc4c[nH]nn4)NC(=O)c5ccc(cn5)NC(=O)c6ccc(cc6)C#N
CACTVS 3.385CC(C)Oc1c(O)c(ccc1NC(=O)c2ccc(NC(=O)[CH](Cc3c[nH]nn3)NC(=O)c4ccc(NC(=O)c5ccc(cc5)C#N)cn4)cn2)C(=O)Nc6ccc(cc6)C(O)=O
FormulaC42 H35 N11 O9
Name4-[[4-[[5-[[(2S)-2-[[5-[(4-cyanophenyl)carbonylamino]pyridin-2-yl]carbonylamino]-3-(1H-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]-2-oxidanyl-3-propan-2-yloxy-phenyl]carbonylamino]benzoic acid
ChEMBL
DrugBank
ZINC
PDB chain7z9m Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7z9m Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		A67 R68 G71 I74
Binding residue
(residue number reindexed from 1)		A60 R61 G64 I67
Annotation score1
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003916 DNA topoisomerase activity
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0034335 DNA negative supercoiling activity
GO:0042802 identical protein binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006261 DNA-templated DNA replication
GO:0006265 DNA topological change
GO:0006351 DNA-templated transcription
GO:0009410 response to xenobiotic stimulus
GO:0046677 response to antibiotic
GO:0051276 chromosome organization
GO:2000104 negative regulation of DNA-templated DNA replication
Cellular Component
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009330 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
GO:0016020 membrane

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7z9m, PDBe:7z9m, PDBj:7z9m
PDBsum7z9m
PubMed36741192
UniProtP0AES4|GYRA_ECOLI DNA gyrase subunit A (Gene Name=gyrA)

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