Structure of PDB 8g5y Chain Lo Binding Site BS03

Receptor Information

>8g5y Chain Lo (length=105) Species: 9606 (Homo sapiens)

VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQ
TKPIFRKKAKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKG
QVIQF

Ligand information

• Ligand ID: 3H3
• InChI: InChI=1S/C26H35NO6/c1-17-10-8-6-4-5-7-9-11-25(32)33-26(17)19(3)12-18(2)22(29)16-21(28)13-20-14-23(30)27-24(31)15-20/h4,6,8-12,17-18,20-21,26,28H,5,7,13-16H2,1-3H3,(H,27,30,31)/b6-4-,10-8+,11-9+,19-12+/t17-,18-,21+,26+/m0/s1
• InChIKey: OYOKHBHOTQDIPM-UGGBQLGDSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: C[C@H]1/C=C/C=C\CC/C=C/C(=O)O[C@H]1/C(=C/[C@H](C)C(=O)C[C@@H](CC2CC(=O)NC(=O)C2)O)/C
  CACTVS 3.385: C[CH]1C=CC=CCCC=CC(=O)O[CH]1C(C)=C[CH](C)C(=O)C[CH](O)CC2CC(=O)NC(=O)C2
  ACDLabs 12.01: O=C1NC(=O)CC(C1)CC(O)CC(=O)C(/C=C(/C2OC(=O)C=CCCC=CC=CC2C)C)C
  OpenEye OEToolkits 1.9.2: CC1C=CC=CCCC=CC(=O)OC1C(=CC(C)C(=O)CC(CC2CC(=O)NC(=O)C2)O)C
  CACTVS 3.385: C[C@H]1/C=C/C=C\CC/C=C/C(=O)O[C@H]1C(/C)=C/[C@H](C)C(=O)C[C@H](O)CC2CC(=O)NC(=O)C2
• Formula: C26 H35 N O6
• Name: 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione
• ZINC: ZINC000263620869
• PDB chain: 8g5y Chain L5 Residue 5523

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g5y mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.29 Å
• Binding residue (original residue number in PDB): X53 P54 F56 K59
• Binding residue (residue number reindexed from 1): X52 P53 F55 K58
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome

External links

• PDB: RCSB:8g5y, PDBe:8g5y, PDBj:8g5y
• PDBsum: 8g5y
• PubMed: 37020024
• UniProt: J3KQN4