Structure of PDB 1kij Chain A Binding Site BS01

Receptor Information
>1kij Chain A (length=384) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEI
LVRLNEDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHSGGKFEQGAY
KVSGGLHGVGASVVNALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGE
APRGKTGTRVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDR
QHGKEEVFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVEVEVGFLH
TQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGP
QPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLL
EILEENPRIAKAVYEKALRAAQAREAARKARELV
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 chain1kij Chain A Residue 400 [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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PDB1kij An open conformation of the Thermus thermophilus gyrase B ATP-binding domain.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N45 E49 D72 R75 G76 I77 P78 D80 I93 V117 R135 T166
Binding residue
(residue number reindexed from 1)		N37 E41 D64 R67 G68 I69 P70 D72 I85 V109 R127 T158
Annotation score1
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
View graph for
Biological Process
External links
PDB RCSB:1kij, PDBe:1kij, PDBj:1kij
PDBsum1kij
PubMed11850422
UniProtQ5SHZ4|GYRB_THET8 DNA gyrase subunit B (Gene Name=gyrB)

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