Structure of PDB 1aj6 Chain A Binding Site BS01

Receptor Information
>1aj6 Chain A (length=194) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIV
TIHADNSVSVQDDGRGIPTGIVSAAEVIMTVLHAGGKFSGGLHGVGVSVV
NALSQKLELVIQHEGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSL
ETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFH
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 chain1aj6 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1aj6 The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N46 R76 I78 P79 I94
Binding residue
(residue number reindexed from 1)		N35 R65 I67 P68 I78
Annotation score1
Binding affinityMOAD: Kd=1.2uM
PDBbind-CN: -logKd/Ki=5.92,Kd=1.2uM
BindingDB: IC50=170nM,Kd=7.0nM,Ki=7.0nM
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
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Biological Process
External links
PDB RCSB:1aj6, PDBe:1aj6, PDBj:1aj6
PDBsum1aj6
PubMed9245398
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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