Structure of PDB 4y16 Chain A Binding Site BS01

Receptor Information

>4y16 Chain A (length=268) Species: 10090 (Mus musculus)

KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQ
GKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCE
MYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQG
TSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPRQLVCHVS
GFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGL
ACRVKHSSLGGQDIILYW

Ligand information

• Ligand ID: FUL
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3+,4+,5-,6-/m0/s1
• InChIKey: SHZGCJCMOBCMKK-KGJVWPDLSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@H]([C@@H]([C@H](O1)O)O)O)O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  CACTVS 3.341: C[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: beta-L-fucopyranose;
  beta-L-fucose;
  6-deoxy-beta-L-galactopyranose;
  L-fucose;
  fucose;
  6-DEOXY-BETA-L-GALACTOSE
• ChEMBL: CHEMBL1230861
• DrugBank: DB03283
• ZINC: ZINC000001532813
• PDB chain: 4y16 Chain F Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4y16 Lipid and Carbohydrate Modifications of alpha-Galactosylceramide Differently Influence Mouse and Human Type I Natural Killer T Cell Activation.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): S114 W129 G130
• Binding residue (residue number reindexed from 1): S109 W124 G125
• Annotation score: 4

External links

• PDB: RCSB:4y16, PDBe:4y16, PDBj:4y16
• PDBsum: 4y16
• PubMed: 26018083
• UniProt: P11609|CD1D1_MOUSE Antigen-presenting glycoprotein CD1d1 (Gene Name=Cd1d1)