Structure of PDB 8cgj Chain L Binding Site BS02

Receptor Information
>8cgj Chain L (length=114) Species: 679895 (Escherichia coli BW25113) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATVNQLVRKPRNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLT
NGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVK
DRKQARSKYGVKRP
Ligand information
Ligand ID5I0
InChIInChI=1S/C21H41N7O13/c1-4-21(37,18(35)36)15(41-16-8(26-2)12(33)9(30)5(3-29)39-16)17(38-4)40-14-7(28-20(24)25)10(31)6(27-19(22)23)11(32)13(14)34/h4-18,26,29-37H,3H2,1-2H3,(H4,22,23,27)(H4,24,25,28)/p+3/t4-,5-,6+,7-,8-,9-,10+,11-,12-,13+,14+,15-,16-,17-,21+/m0/s1
InChIKeyATLHDHNZEMANQF-UQHZJGBMSA-Q
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1C(C(C(O1)OC2C(C(C(C(C2O)O)NC(=[NH2+])N)O)NC(=[NH2+])N)OC3C(C(C(C(O3)CO)O)O)[NH2+]C)(C(O)O)O
CACTVS 3.385C[NH2+][CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[CH]2[CH](O[CH](C)[C]2(O)C(O)O)O[CH]3[CH](O)[CH](O)[CH](NC(N)=[NH2+])[CH](O)[CH]3NC(N)=[NH2+]
CACTVS 3.385C[NH2+][C@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O[C@H]2[C@@H](O[C@@H](C)[C@]2(O)C(O)O)O[C@H]3[C@H](O)[C@@H](O)[C@H](NC(N)=[NH2+])[C@@H](O)[C@@H]3NC(N)=[NH2+]
OpenEye OEToolkits 2.0.7C[C@H]1[C@@]([C@H]([C@@H](O1)O[C@@H]2[C@H]([C@@H]([C@H]([C@@H]([C@H]2O)O)NC(=[NH2+])N)O)NC(=[NH2+])N)O[C@H]3[C@H]([C@@H]([C@H]([C@@H](O3)CO)O)O)[NH2+]C)(C(O)O)O
FormulaC21 H44 N7 O13
Name[(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[(1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium;
hydrated form of streptomycin
ChEMBL
DrugBank
ZINC
PDB chain8cgj Chain A Residue 1603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8cgj Structural conservation of antibiotic interaction with ribosomes.
Resolution1.79 Å
Binding residue
(original residue number in PDB)
K43 K88
Binding residue
(residue number reindexed from 1)
K35 K80
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0034336 misfolded RNA binding
Biological Process
GO:0000372 Group I intron splicing
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0033120 positive regulation of RNA splicing
GO:0034337 RNA folding
GO:0046677 response to antibiotic
GO:1990145 maintenance of translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8cgj, PDBe:8cgj, PDBj:8cgj
PDBsum8cgj
PubMed37550453
UniProtP0A7S3|RS12_ECOLI Small ribosomal subunit protein uS12 (Gene Name=rpsL)

[Back to BioLiP]