Structure of PDB 4urm Chain B Binding Site BS01

Receptor Information
>4urm Chain B (length=195) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKD
NWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGVGSSVVNALSQ
DLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTE
TTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG
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
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]
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)
I51 N54 E58 D81 I86 Q91 K93 I102 H107 A108 G109 G110 T173
Binding residue
(residue number reindexed from 1)
I27 N30 E34 D57 I62 Q67 K69 I78 H83 A84 G85 G86 T137
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

View graph for
Molecular Function

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

[Back to BioLiP]