Structure of PDB 8sgm Chain A Binding Site BS01

Receptor Information

>8sgm Chain A (length=271) Species: 9606 (Homo sapiens)

RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQ
GTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYLELQVSAGCEVHP
GNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRE
TVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVC
HVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGEA
AGLSCRVKHSSLEGQDIVLYQ

Ligand information

• Ligand ID: A1AHF
• InChI: InChI=1S/C46H89NO8/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-24-26-28-30-32-34-36-42(50)47-39(38-54-46-45(53)44(52)43(51)41(37-48)55-46)40(49)35-33-31-29-27-25-23-16-14-12-10-8-6-4-2/h39,41,43-46,48,51-53H,3-38H2,1-2H3,(H,47,50)/t39-,41-,43+,44+,45+,46-/m0/s1
• InChIKey: HKCYWBHIRZDQLD-HMGLXMNBSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCCCCCCCCCC(=O)N[C@H](CO[C@H]1[C@@H]([C@@H]([C@@H]([C@H](O1)CO)O)O)O)C(=O)CCCCCCCCCCCCCCC
  ACDLabs 12.01: CCCCCCCCCCCCCCCC(=O)C(COC1OC(CO)C(O)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCC
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(=O)CCCCCCCCCCCCCCC
  CACTVS 3.385: CCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)C(=O)CCCCCCCCCCCCCCC
  CACTVS 3.385: CCCCCCCCCCCCCCCCCCCCCC(=O)N[C@H](CO[C@@H]1O[C@H](CO)[C@@H](O)[C@@H](O)[C@H]1O)C(=O)CCCCCCCCCCCCCCC
• Formula: C46 H89 N O8
• Name: N-[(2S)-3-oxo-1-(beta-L-talopyranosyloxy)octadecan-2-yl]docosanamide
• PDB chain: 8sgm Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8sgm Semi-invariant human type II Natural Killer T cells recognise CD1d independently of bound lipids.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): Q14 L29 W40 F70 Y73 S76 D80 F114 D151 W153 T154 F169
• Binding residue (residue number reindexed from 1): Q9 L24 W35 F65 Y68 S71 D75 F108 D145 W147 T148 F163
• Annotation score: 1

External links

• PDB: RCSB:8sgm, PDBe:8sgm, PDBj:8sgm
• PDBsum: 8sgm
• UniProt: P15813|CD1D_HUMAN Antigen-presenting glycoprotein CD1d (Gene Name=CD1D)