Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP

Structure of PDB 5d6q Chain B Binding Site BS01

Receptor Information
>5d6q Chain B (length=186) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEV
VIEKDNWIKVTDNGRGIPVDIQGRPAVEVILTSSVVNALSQDLEVYVHRN
ETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETL
QQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG
Ligand information
Ligand ID57V
InChIInChI=1S/C17H17N5OS/c1-2-19-16(23)22-17-21-14(8-7-12-5-3-9-18-11-12)15(24-17)13-6-4-10-20-13/h3-11,20H,2H2,1H3,(H2,19,21,22,23)/b8-7+
InChIKeyKXSSNSOHTLLWNT-BQYQJAHWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCNC(=O)Nc1sc(c2[nH]ccc2)c(C=Cc3cccnc3)n1
CACTVS 3.385CCNC(=O)Nc1sc(c2[nH]ccc2)c(/C=C/c3cccnc3)n1
OpenEye OEToolkits 1.9.2CCNC(=O)Nc1nc(c(s1)c2ccc[nH]2)/C=C/c3cccnc3
OpenEye OEToolkits 1.9.2CCNC(=O)Nc1nc(c(s1)c2ccc[nH]2)C=Cc3cccnc3
ACDLabs 12.01O=C(NCC)Nc2sc(c(\C=C\c1cccnc1)n2)c3nccc3
FormulaC17 H17 N5 O S
Name1-ethyl-3-{4-[(E)-2-(pyridin-3-yl)ethenyl]-5-(1H-pyrrol-2-yl)-1,3-thiazol-2-yl}urea
ChEMBLCHEMBL3736029
DrugBank
ZINCZINC000263620681
PDB chain5d6q Chain B Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5d6q Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		N54 D81 R84 I86 P87 I102 R144
Binding residue
(residue number reindexed from 1)		N35 D62 R65 I67 P68 I80 R99
Annotation score1
Binding affinityMOAD: ic50=5.8uM
PDBbind-CN: -logKd/Ki=5.24,IC50=5.8uM
BindingDB: IC50=5800nM
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:5d6q, PDBe:5d6q, PDBj:5d6q
PDBsum5d6q
PubMed26460684
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB)

[Back to BioLiP]

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417