Structure of PDB 1kzn Chain A Binding Site BS01

Receptor Information
>1kzn Chain A (length=186) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIH
ADNSVSVQDDGRGIPTGIGVSAAEVIMTVLHAHGVGVSVVNALSQKLELV
IQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFE
YEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYE
Ligand information
Ligand IDCBN
InChIInChI=1S/C35H37ClN2O11/c1-16(2)7-9-18-15-19(10-13-22(18)39)31(42)38-25-26(40)20-11-14-23(24(36)28(20)47-33(25)44)46-34-27(41)29(30(45-6)35(4,5)49-34)48-32(43)21-12-8-17(3)37-21/h7-8,10-15,27,29-30,34,37,39-41H,9H2,1-6H3,(H,38,42)/t27-,29+,30-,34-/m1/s1
InChIKeyFJAQNRBDVKIIKK-LFLQOBSNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1ccc([nH]1)C(=O)O[C@H]2[C@H]([C@@H](OC([C@@H]2OC)(C)C)Oc3ccc4c(c3Cl)OC(=O)C(=C4O)NC(=O)c5ccc(c(c5)CC=C(C)C)O)O
ACDLabs 10.04O=C(c1ccc(O)c(c1)C\C=C(/C)C)NC4=C(O)c5ccc(OC3OC(C(OC)C(OC(=O)c2ccc(n2)C)C3O)(C)C)c(Cl)c5OC4=O
CACTVS 3.341CO[C@@H]1[C@@H](OC(=O)c2[nH]c(C)cc2)[C@@H](O)[C@H](Oc3ccc4C(=C(NC(=O)c5ccc(O)c(CC=C(C)C)c5)C(=O)Oc4c3Cl)O)OC1(C)C
OpenEye OEToolkits 1.5.0Cc1ccc([nH]1)C(=O)OC2C(C(OC(C2OC)(C)C)Oc3ccc4c(c3Cl)OC(=O)C(=C4O)NC(=O)c5ccc(c(c5)CC=C(C)C)O)O
CACTVS 3.341CO[CH]1[CH](OC(=O)c2[nH]c(C)cc2)[CH](O)[CH](Oc3ccc4C(=C(NC(=O)c5ccc(O)c(CC=C(C)C)c5)C(=O)Oc4c3Cl)O)OC1(C)C
FormulaC35 H37 Cl N2 O11
NameCLOROBIOCIN
ChEMBLCHEMBL303984
DrugBankDB03966
ZINCZINC000004102306
PDB chain1kzn Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1kzn DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N46 E50 V71 D73 R76 G77 I78 P79 I90 R136 T165
Binding residue
(residue number reindexed from 1)		N32 E36 V57 D59 R62 G63 I64 P65 I76 R103 T132
Annotation score1
Binding affinityMOAD: Kd=1.2nM
PDBbind-CN: -logKd/Ki=8.92,Kd=1.2nM
BindingDB: IC50=73nM
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
Biological Process
GO:0006265 DNA topological change

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1kzn, PDBe:1kzn, PDBj:1kzn
PDBsum1kzn
PubMed12044152
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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