Structure of PDB 4urm Chain C Binding Site BS01

Receptor Information
>4urm Chain C (length=191) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKD
NWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGVGSSVVNALSQDLEV
YVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVY
NYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG
Ligand information
Ligand IDXAM
InChIInChI=1S/C44H60Cl2N4O14/c1-16(2)33-35(53)29(41(56)50(33)42-38(59-10)37(62-23(9)51)36(20(6)61-42)64-43(47)57)34(52)28-18(4)11-13-24-25(14-12-17(3)27(24)28)63-26-15-44(58,39(54)21(7)60-26)22(8)49-40(55)32-31(46)30(45)19(5)48-32/h11,13,16,18,20-22,24-28,33,36-39,42,48,53-54,58H,3,12,14-15H2,1-2,4-10H3,(H2,47,57)(H,49,55)/t18-,20-,21+,22-,24-,25+,26-,27-,28-,33-,36+,37+,38+,39+,42+,44+/m0/s1
InChIKeyQOFXLOGWNULKEG-FHIRBROQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c(c(c([nH]1)C(=O)NC(C)C2(CC(OC(C2O)C)OC3CCC(=C)C4C3C=CC(C4C(=O)C5=C(C(N(C5=O)C6C(C(C(C(O6)C)OC(=O)N)OC(=O)C)OC)C(C)C)O)C)O)Cl)Cl
ACDLabs 12.01O=C(OC1C(OC)C(OC(C)C1OC(=O)N)N2C(=O)C(=C(O)C2C(C)C)C(=O)C6C(C=CC5C(OC3OC(C(O)C(O)(C3)C(NC(=O)c4c(Cl)c(Cl)c(n4)C)C)C)CC/C(=C)C56)C)C
CACTVS 3.370CO[C@@H]1[C@H](OC(C)=O)[C@H](OC(N)=O)[C@H](C)O[C@H]1N2[C@@H](C(C)C)C(=C(C(=O)[C@H]3[C@@H](C)C=C[C@H]4[C@@H](CCC(=C)[C@H]34)O[C@H]5C[C@@](O)([C@H](C)NC(=O)c6[nH]c(C)c(Cl)c6Cl)[C@H](O)[C@@H](C)O5)C2=O)O
OpenEye OEToolkits 1.7.6Cc1c(c(c([nH]1)C(=O)N[C@@H](C)[C@@]2(C[C@@H](O[C@@H]([C@H]2O)C)O[C@@H]3CCC(=C)[C@H]4[C@H]3C=C[C@@H]([C@@H]4C(=O)C5=C([C@@H](N(C5=O)[C@H]6[C@@H]([C@@H]([C@@H]([C@@H](O6)C)OC(=O)N)OC(=O)C)OC)C(C)C)O)C)O)Cl)Cl
CACTVS 3.370CO[CH]1[CH](OC(C)=O)[CH](OC(N)=O)[CH](C)O[CH]1N2[CH](C(C)C)C(=C(C(=O)[CH]3[CH](C)C=C[CH]4[CH](CCC(=C)[CH]34)O[CH]5C[C](O)([CH](C)NC(=O)c6[nH]c(C)c(Cl)c6Cl)[CH](O)[CH](C)O5)C2=O)O
FormulaC44 H60 Cl2 N4 O14
Name(1R,4aS,5S,6S,8aR)-5-{[(5S)-1-(3-O-acetyl-4-O-carbamoyl-6-deoxy-2-O-methyl-alpha-L-talopyranosyl)-4-hydroxy-2-oxo-5-(propan-2-yl)-2,5-dihydro-1H-pyrrol-3-yl]carbonyl}-6-methyl-4-methylidene-1,2,3,4,4a,5,6,8a-octahydronaphthalen-1-yl 2,6-dideoxy-3-C-[(1S)-1-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}ethyl]-beta-D-ribo-hexopyranoside;
Amycolamicin
ChEMBL
DrugBank
ZINCZINC000263620947
PDB chain4urm Chain B Residue 2000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4urm Structures of Kibdelomycin Bound to Staphylococcus Aureus Gyrb and Pare Showed a Novel U-Shaped Binding Mode.
Resolution2.94 Å
Binding residue
(original residue number in PDB)
R200 E201 F204
Binding residue
(residue number reindexed from 1)
R160 E161 F164
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

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Biological Process
External links
PDB RCSB:4urm, PDBe:4urm, PDBj:4urm
PDBsum4urm
PubMed24992706
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB)

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