Structure of PDB 5obm Chain l3 Binding Site BS06

Receptor Information
>5obm Chain l3 (length=386) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKA
GMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRS
LTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARI
KKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEK
TVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVAC
IGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKAL
EEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL
Ligand information
Ligand IDLLL
InChIInChI=1S/C19H39N5O7/c1-19(27)7-28-18(13(26)16(19)24-2)31-15-11(23)5-10(22)14(12(15)25)30-17-9(21)4-3-8(6-20)29-17/h8-18,24-27H,3-7,20-23H2,1-2H3/t8-,9+,10-,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1
InChIKeyVEGXETMJINRLTH-BOZYPMBZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN[CH]1[CH](O)[CH](OC[C]1(C)O)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CN)CC[CH]3N)[CH]2O
ACDLabs 10.04O(C2C(O)C(OC1OC(CN)CCC1N)C(N)CC2N)C3OCC(O)(C(NC)C3O)C
OpenEye OEToolkits 1.5.0CC1(COC(C(C1NC)O)OC2C(CC(C(C2O)OC3C(CCC(O3)CN)N)N)N)O
OpenEye OEToolkits 1.5.0C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H](CC[C@H](O3)CN)N)N)N)O
CACTVS 3.341CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)CC[C@H]3N)[C@@H]2O
FormulaC19 H39 N5 O7
Name(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL;
GENTAMICIN C1A
ChEMBLCHEMBL194126
DrugBankDB04729
ZINCZINC000008216590
PDB chain5obm Chain l3 Residue 412 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5obm Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		R167 T169 P170 L171 A172
Binding residue
(residue number reindexed from 1)		R166 T168 P169 L170 A171
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0002181 cytoplasmic translation
GO:0006364 rRNA processing
GO:0006412 translation
GO:0006414 translational elongation
GO:1990145 maintenance of translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5obm, PDBe:5obm, PDBj:5obm
PDBsum5obm
PubMed29208708
UniProtP14126|RL3_YEAST Large ribosomal subunit protein uL3 (Gene Name=RPL3)

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