Structure of PDB 3sdx Chain C Binding Site BS01

Receptor Information
>3sdx Chain C (length=268) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQ
GTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVH
PGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTR
ETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLV
CHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGE
SCRVKHSSLEGQDIVLYW
Ligand information
Ligand IDGCY
InChIInChI=1S/C48H93NO8/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-44(52)49-41(40-56-48-47(55)46(54)45(53)43(39-50)57-48)42(51)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h35,37,41-43,45-48,50-51,53-55H,3-34,36,38-40H2,1-2H3,(H,49,52)/b37-35+/t41-,42+,43+,45-,46-,47+,48+/m0/s1
InChIKeyPOQRWMRXUOPCLD-HIIAJUEOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(C=CCCCCCCCCCCCCC)O
CACTVS 3.370CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)[C@H](O)/C=C/CCCCCCCCCCCCC
ACDLabs 12.01O=C(NC(COC1OC(C(O)C(O)C1O)CO)C(O)/C=C/CCCCCCCCCCCCC)CCCCCCCCCCCCCCCCCCCCCCC
CACTVS 3.370CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O)[CH](O)C=CCCCCCCCCCCCCC
OpenEye OEToolkits 1.7.2CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O)[C@@H](C=CCCCCCCCCCCCCC)O
FormulaC48 H93 N O8
NameN-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide;
beta-Galactosylceramide, Ceramide beta-D-galactoside
ChEMBL
DrugBank
ZINCZINC000085551900
PDB chain3sdx Chain C Residue 602 [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]
PDB3sdx Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors
Resolution3.12 Å
Binding residue
(original residue number in PDB)		C12 Q14 Y73 S76 F114 D151 W153 T154
Binding residue
(residue number reindexed from 1)		C7 Q9 Y68 S71 F109 D146 W148 T149
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:3sdx, PDBe:3sdx, PDBj:3sdx
PDBsum3sdx
PubMed21804559
UniProtP15813|CD1D_HUMAN Antigen-presenting glycoprotein CD1d (Gene Name=CD1D)

[Back to BioLiP]