Structure of PDB 4urm Chain D Binding Site BS01

Receptor Information
>4urm Chain D (length=190) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDN
WIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGVGSSVVNALSQDLEVY
VHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYN
YETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG
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 D 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)
N54 E58 D81 R84 I86 I102 V105 H107 A108 T173 I175
Binding residue
(residue number reindexed from 1)
N29 E33 D56 R59 I61 I77 V80 H82 A83 T132 I134
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)

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