Structure of PDB 5iqc Chain D Binding Site BS02

Receptor Information
>5iqc Chain D (length=290) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YDDNATNVKAMKYLIEHYFDNFKVDSIEIIGDSVAYLVNNEYIFKTKFSY
AKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIY
STMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRE
TIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNR
LTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKA
KEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTY
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 chain5iqc 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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PDB5iqc Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
D374 S376 Y408 E411 E415 E416 E445 Y448 E451
Binding residue
(residue number reindexed from 1)
D187 S189 Y221 E224 E228 E229 E258 Y261 E264
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.1.-
2.7.1.190: aminoglycoside 2''-phosphotransferase.
External links
PDB RCSB:5iqc, PDBe:5iqc, PDBj:5iqc
PDBsum5iqc
PubMed27161980
UniProtP0A0C1|AACA_STAAU Bifunctional AAC/APH (Gene Name=aacA-aphD)

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