Structure of PDB 2b0q Chain A Binding Site BS01

Receptor Information
>2b0q Chain A (length=263) Species: 1351 (Enterococcus faecalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYK
GTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEE
YEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDL
ADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDG
KVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDW
EKIKYYILLDELF
Ligand information
Ligand IDNMY
InChIInChI=1S/C23H46N6O13/c24-2-7-13(32)15(34)10(28)21(37-7)40-18-6(27)1-5(26)12(31)20(18)42-23-17(36)19(9(4-30)39-23)41-22-11(29)16(35)14(33)8(3-25)38-22/h5-23,30-36H,1-4,24-29H2/t5-,6+,7-,8+,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1
InChIKeyPGBHMTALBVVCIT-VCIWKGPPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)N)OC3C(C(C(O3)CO)OC4C(C(C(C(O4)CN)O)O)N)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]4O[CH](CN)[CH](O)[CH](O)[CH]4N)[CH]3O)[CH](N)[CH](O)[CH]1O
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[C@@H]4[C@@H]([C@H]([C@@H]([C@@H](O4)CN)O)O)N)O)O)N
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]4O[C@@H](CN)[C@@H](O)[C@H](O)[C@H]4N)[C@H]3O)[C@H](N)[C@@H](O)[C@@H]1O
ACDLabs 10.04O(C2C(OC1OC(CN)C(O)C(O)C1N)C(N)CC(N)C2O)C4OC(C(OC3OC(CN)C(O)C(O)C3N)C4O)CO
FormulaC23 H46 N6 O13
NameNEOMYCIN;
MYCIFRADIN;
NEOMAS;
PIMAVECORT;
VONAMYCIN
ChEMBLCHEMBL184618
DrugBankDB00452
ZINCZINC000071928291
PDB chain2b0q Chain A Residue 305 [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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PDB2b0q Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		E24 E157 N158 E160 D190 D193 S194 E230 D231 D261 E262 F264
Binding residue
(residue number reindexed from 1)		E23 E156 N157 E159 D189 D192 S193 E229 D230 D260 E261 F263
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K44 D190 N195 D208
Catalytic site (residue number reindexed from 1) K43 D189 N194 D207
Enzyme Commision number 2.7.1.95: kanamycin kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008910 kanamycin kinase activity
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
Biological Process
GO:0016310 phosphorylation
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2b0q, PDBe:2b0q, PDBj:2b0q
PDBsum2b0q
PubMed12006485
UniProtP0A3Y5|KKA3_ENTFL Aminoglycoside 3'-phosphotransferase (Gene Name=aphA)

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