Structure of PDB 6cav Chain D Binding Site BS03

Receptor Information
>6cav Chain D (length=284) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATNVKAMKYLIEHYFDNFKVDSIEIIGSSVAYLVNNEYIFKTKFYAKEKA
IYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSE
EEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYND
LTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGII
DFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQD
IVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRT
Ligand information
Ligand ID84D
InChIInChI=1S/C18H37N5O8/c19-4-6-1-2-7(20)17(28-6)30-15-8(21)3-9(22)16(14(15)27)31-18-13(26)11(23)12(25)10(5-24)29-18/h6-18,24-27H,1-5,19-23H2/t6-,7+,8-,9+,10+,11-,12+,13+,14-,15+,16-,17+,18+/m0/s1
InChIKeyJJCQSGDBDPYCEO-XVZSLQNASA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC[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]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O
OpenEye OEToolkits 2.0.6C1CC(C(OC1CN)OC2C(CC(C(C2O)OC3C(C(C(C(O3)CO)O)N)O)N)N)N
CACTVS 3.385NC[CH]1CC[CH](N)[CH](O1)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O
OpenEye OEToolkits 2.0.6C1C[C@H]([C@H](O[C@@H]1CN)O[C@@H]2[C@H](C[C@H]([C@@H]([C@H]2O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)N)O)N)N)N
ACDLabs 12.01C3C(N)C(OC2C(N)CC(C(OC1OC(C(O)C(C1O)N)CO)C2O)N)OC(C3)CN
FormulaC18 H37 N5 O8
NameDibekacin;
(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside
ChEMBLCHEMBL560976
DrugBankDB13270
ZINCZINC000008214383
PDB chain6cav 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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PDB6cav Plasticity of Aminoglycoside Binding to Antibiotic Kinase APH(2′′)-Ia.
Resolution2.6 Å
Binding residue
(original residue number in PDB)
D374 S376 D396 Y408 E411 E415 E416 Y448 E451
Binding residue
(residue number reindexed from 1)
D182 S184 D204 Y216 E219 E223 E224 Y256 E259
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.1.-
2.7.1.190: aminoglycoside 2''-phosphotransferase.
External links
PDB RCSB:6cav, PDBe:6cav, PDBj:6cav
PDBsum6cav
PubMed29661878
UniProtP0A0C1|AACA_STAAU Bifunctional AAC/APH (Gene Name=aacA-aphD)

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