Structure of PDB 8ijq Chain B Binding Site BS01

Receptor Information
>8ijq Chain B (length=264) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLDPEYWKTILSCIYVFIVFGFTSFIMVIVHERVPDMQTYPPLPDIFLDS
VPRIPWAFAMTEVCGMILCYIWLLVLLLHKHRSILLRRLCSLMGTVFLLR
CFTMFVTSLSVPGQHLQCTGKIYGSVWEKLHRAFAIWSGFGMTLTGVHTC
GDYMFSGHTVVLTMLNFFVTEYTPRSWNFLHTLSWVLNLFGIFFILAAHE
HYSIDVFIAFYITTRLFLYYHTLANTRAYQQSRRARIWFPMFSFFECNVN
GTVPNEYCWPFSKP
Ligand information
Ligand ID16C
InChIInChI=1S/C34H67NO3/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-33(37)32(31-36)35-34(38)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h27,29,32-33,36-37H,3-26,28,30-31H2,1-2H3,(H,35,38)/b29-27+/t32-,33+/m0/s1
InChIKeyYDNKGFDKKRUKPY-TURZORIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCC(=O)NC(CO)C(C=CCCCCCCCCCCCCC)O
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@@H](\C=C\CCCCCCCCCCCCC)O
ACDLabs 10.04O=C(NC(CO)C(O)/C=C/CCCCCCCCCCCCC)CCCCCCCCCCCCCCC
CACTVS 3.341CCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)\C=C\CCCCCCCCCCCCC
CACTVS 3.341CCCCCCCCCCCCCCCC(=O)N[CH](CO)[CH](O)C=CCCCCCCCCCCCCC
FormulaC34 H67 N O3
NameN-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE;
C16-CERAMIDE;
N-PALMITOYL-D-ERYTHRO-SPHINGOSINE;
(2S,3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL;
(2S,3R,4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL
ChEMBLCHEMBL35292
DrugBank
ZINCZINC000008860497
PDB chain8ijq Chain B Residue 500 [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]
PDB8ijq Cryo-EM structure of human sphingomyelin synthase and its mechanistic implications for sphingomyelin synthesis.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		F163 M170 M236 R243 F283 D295 G300 H301 V304
Binding residue
(residue number reindexed from 1)		F20 M27 M93 R100 F140 D152 G157 H158 V161
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.8.-
Gene Ontology
Molecular Function
GO:0016780 phosphotransferase activity, for other substituted phosphate groups

View graph for
Molecular Function
External links
PDB RCSB:8ijq, PDBe:8ijq, PDBj:8ijq
PDBsum8ijq
PubMed38388831
UniProtQ96LT4|SAMD8_HUMAN Sphingomyelin synthase-related protein 1 (Gene Name=SAMD8)

[Back to BioLiP]