Structure of PDB 8k2c Chain SF Binding Site BS03

Receptor Information
>8k2c Chain SF (length=184) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQ
CPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNA
IINSGPREDSTRIGRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIA
ECLADELINAAKGSSNSYAIKKKDELERVAKSNR
Ligand information
Ligand IDT1C
InChIInChI=1S/C29H39N5O8/c1-28(2,3)31-11-17(35)32-15-10-16(33(4)5)13-8-12-9-14-21(34(6)7)24(38)20(27(30)41)26(40)29(14,42)25(39)18(12)23(37)19(13)22(15)36/h10,12,14,21,31,36,38-39,42H,8-9,11H2,1-7H3,(H2,30,41)(H,32,35)/p+2/t12-,14-,21-,29-/m0/s1
InChIKeyFPZLLRFZJZRHSY-HJYUBDRYSA-P
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC(C)(C)NCC(=O)Nc1cc(c2c(c1O)C(=O)C3=C([C@]4([C@@H](C[C@@H]3C2)[C@@H](C(=C(C4=O)C(=O)N)O)[NH+](C)C)O)O)[NH+](C)C
CACTVS 3.385C[NH+](C)[CH]1[CH]2C[CH]3Cc4c(cc(NC(=O)CNC(C)(C)C)c(O)c4C(=O)C3=C(O)[C]2(O)C(=O)C(=C1O)C(N)=O)[NH+](C)C
OpenEye OEToolkits 1.9.2CC(C)(C)NCC(=O)Nc1cc(c2c(c1O)C(=O)C3=C(C4(C(CC3C2)C(C(=C(C4=O)C(=O)N)O)[NH+](C)C)O)O)[NH+](C)C
CACTVS 3.385C[NH+](C)[C@H]1[C@@H]2C[C@@H]3Cc4c(cc(NC(=O)CNC(C)(C)C)c(O)c4C(=O)C3=C(O)[C@]2(O)C(=O)C(=C1O)C(N)=O)[NH+](C)C
ACDLabs 12.01O=C2C1=C(O)C4(O)C(=O)C(=C(O)C(C4CC1Cc3c2c(O)c(NC(=O)CNC(C)(C)C)cc3[NH+](C)C)[NH+](C)C)C(=O)N
FormulaC29 H41 N5 O8
NameTIGECYCLINE
ChEMBL
DrugBank
ZINC
PDB chain8k2c Chain S2 Residue 1930 [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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PDB8k2c Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		N148 Q149 W152
Binding residue
(residue number reindexed from 1)		N128 Q129 W132
Annotation score1
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0006413 translational initiation
GO:0006450 regulation of translational fidelity
GO:0042274 ribosomal small subunit biogenesis
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0032040 small-subunit processome
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8k2c, PDBe:8k2c, PDBj:8k2c
PDBsum8k2c
PubMed38942792
UniProtP46782|RS5_HUMAN Small ribosomal subunit protein uS7 (Gene Name=RPS5)

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