Structure of PDB 5iqd Chain A Binding Site BS02

Receptor Information
>5iqd Chain A (length=296) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKF
SKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLT
PEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYI
LLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLD
GNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNID
IEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD
Ligand information
Ligand IDRIO
InChIInChI=1S/C17H34N4O10/c18-2-6-10(24)12(26)8(21)16(28-6)30-14-5(20)1-4(19)9(23)15(14)31-17-13(27)11(25)7(3-22)29-17/h4-17,22-27H,1-3,18-21H2/t4-,5+,6-,7-,8-,9+,10-,11-,12-,13-,14-,15-,16-,17+/m1/s1
InChIKeyNSKGQURZWSPSBC-VVPCINPTSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O(C2C(OC1OC(CN)C(O)C(O)C1N)C(N)CC(N)C2O)C3OC(C(O)C3O)CO
OpenEye OEToolkits 1.5.0C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)N)OC3C(C(C(O3)CO)O)O)O)N
OpenEye OEToolkits 1.5.0C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CN)O)O)N)O[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)O)N
CACTVS 3.341NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O)[CH]2O[CH]3O[CH](CO)[CH](O)[CH]3O)[CH](N)[CH](O)[CH]1O
CACTVS 3.341NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)[C@H](N)[C@@H](O)[C@@H]1O
FormulaC17 H34 N4 O10
NameRIBOSTAMYCIN;
5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL;
(1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
ChEMBLCHEMBL221572
DrugBankDB03615
ZINCZINC000053255716
PDB chain5iqd Chain A Residue 600 [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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PDB5iqd Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia.
Resolution2.2 Å
Binding residue
(original residue number in PDB)
D374 S376 Y408 E411 E415 E416 V444 E445 Y448 E451
Binding residue
(residue number reindexed from 1)
D191 S193 Y225 E228 E232 E233 V261 E262 Y265 E268
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.1.-
2.7.1.190: aminoglycoside 2''-phosphotransferase.
External links
PDB RCSB:5iqd, PDBe:5iqd, PDBj:5iqd
PDBsum5iqd
PubMed27161980
UniProtP0A0C1|AACA_STAAU Bifunctional AAC/APH (Gene Name=aacA-aphD)

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