Structure of PDB 5iqg Chain D Binding Site BS02

Receptor Information
>5iqg Chain D (length=301) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKT
KFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEI
KGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQN
VLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSC
NHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILR
MYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTY
K
Ligand information
Ligand ID51G
InChIInChI=1S/C21H43N5O7/c1-9(25-3)13-6-5-10(22)19(31-13)32-16-11(23)7-12(24)17(14(16)27)33-20-15(28)18(26-4)21(2,29)8-30-20/h9-20,25-29H,5-8,22-24H2,1-4H3/t9-,10-,11+,12-,13+,14+,15-,16-,17+,18-,19-,20-,21+/m1/s1
InChIKeyCEAZRRDELHUEMR-CAMVTXANSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01OC1C(NC)C(C)(O)COC1OC2C(CC(N)C(C2O)OC3OC(CCC3N)C(NC)C)N
OpenEye OEToolkits 1.9.2CC(C1CCC(C(O1)OC2C(CC(C(C2O)OC3C(C(C(CO3)(C)O)NC)O)N)N)N)NC
CACTVS 3.385CN[CH](C)[CH]1CC[CH](N)[CH](O1)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3OC[C](C)(O)[CH](NC)[CH]3O)[CH]2O
OpenEye OEToolkits 1.9.2C[C@H]([C@@H]1CC[C@H]([C@H](O1)O[C@@H]2[C@H](C[C@H]([C@@H]([C@H]2O)O[C@@H]3[C@@H]([C@H]([C@@](CO3)(C)O)NC)O)N)N)N)NC
CACTVS 3.385CN[C@H](C)[C@@H]1CC[C@@H](N)[C@H](O1)O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3OC[C@](C)(O)[C@H](NC)[C@H]3O)[C@H]2O
FormulaC21 H43 N5 O7
Namegentamicin C1;
(1S,2S,3R,4S,6R)-4,6-diamino-3-({(2R,3R,6S)-3-amino-6-[(1R)-1-(methylamino)ethyl]tetrahydro-2H-pyran-2-yl}oxy)-2-hydrox ycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside
ChEMBLCHEMBL463809
DrugBank
ZINCZINC000008143541
PDB chain5iqg Chain D 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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PDB5iqg Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia.
Resolution2.5 Å
Binding residue
(original residue number in PDB)
D374 S376 D396 Y408 E411 E415 E416 E445 Y448 E451
Binding residue
(residue number reindexed from 1)
D197 S199 D219 Y231 E234 E238 E239 E268 Y271 E274
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.1.-
2.7.1.190: aminoglycoside 2''-phosphotransferase.
External links
PDB RCSB:5iqg, PDBe:5iqg, PDBj:5iqg
PDBsum5iqg
PubMed27161980
UniProtP0A0C1|AACA_STAAU Bifunctional AAC/APH (Gene Name=aacA-aphD)

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