Structure of PDB 4uro Chain A Binding Site BS01

Receptor Information
>4uro Chain A (length=187) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDN
WIKVTDNGRGIPVDIQEKMGRPAVEVILTVGVGSSVVNALSQDLEVYVHR
NETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYET
LQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG
Ligand information
Ligand IDNOV
InChIInChI=1S/C31H36N2O11/c1-14(2)7-8-16-13-17(9-11-19(16)34)27(37)33-21-22(35)18-10-12-20(15(3)24(18)42-28(21)38)41-29-23(36)25(43-30(32)39)26(40-6)31(4,5)44-29/h7,9-13,23,25-26,29,34-36H,8H2,1-6H3,(H2,32,39)(H,33,37)/t23-,25+,26-,29-/m1/s1
InChIKeyYJQPYGGHQPGBLI-KGSXXDOSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)c3ccc(c(c3)CC=C(C)C)O)O[C@H]4[C@@H]([C@@H]([C@H](C(O4)(C)C)OC)OC(=O)N)O
CACTVS 3.370CO[CH]1[CH](OC(N)=O)[CH](O)[CH](Oc2ccc3C(=C(NC(=O)c4ccc(O)c(CC=C(C)C)c4)C(=O)Oc3c2C)O)OC1(C)C
ACDLabs 12.01O=C(c1ccc(O)c(c1)C\C=C(/C)C)NC3=C(O)c4ccc(OC2OC(C(OC)C(OC(=O)N)C2O)(C)C)c(c4OC3=O)C
CACTVS 3.370CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](Oc2ccc3C(=C(NC(=O)c4ccc(O)c(CC=C(C)C)c4)C(=O)Oc3c2C)O)OC1(C)C
OpenEye OEToolkits 1.7.0Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)c3ccc(c(c3)CC=C(C)C)O)OC4C(C(C(C(O4)(C)C)OC)OC(=O)N)O
FormulaC31 H36 N2 O11
NameNOVOBIOCIN;
4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside
ChEMBLCHEMBL36506
DrugBankDB01051
ZINCZINC000014879999
PDB chain4uro Chain A Residue 2000 [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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PDB4uro Structures of Kibdelomycin Bound to Staphylococcus Aureus Gyrb and Pare Showed a Novel U-Shaped Binding Mode.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		N54 S55 E58 D81 R84 I86 P87 D89 I102 R144
Binding residue
(residue number reindexed from 1)		N29 S30 E33 D56 R59 I61 P62 D64 I77 R100
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.40,IC50<4nM
BindingDB: IC50=41nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4uro, PDBe:4uro, PDBj:4uro
PDBsum4uro
PubMed24992706
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB)

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