Structure of PDB 8ijr Chain D Binding Site BS01

Receptor Information
>8ijr Chain D (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 IDZ0P
InChIInChI=1S/C37H70O5/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-37(40)42-35(33-38)34-41-36(39)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h13,15,35,38H,3-12,14,16-34H2,1-2H3/b15-13-/t35-/m0/s1
InChIKeyIIEPDWHEGOSXLD-NMYQGLQJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCCC(=O)OCC(CO)OC(=O)CCCCCCCCCC=CCCCCCC
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCCC(=O)OC[C@H](CO)OC(=O)CCCCCCCCC/C=C\CCCCCC
ACDLabs 12.01O=C(OC(CO)COC(=O)CCCCCCCCCCCCCCC)CCCCCCCCC\C=C/CCCCCC
CACTVS 3.370CCCCCCCCCCCCCCCC(=O)OC[C@H](CO)OC(=O)CCCCCCCCC\C=C/CCCCCC
CACTVS 3.370CCCCCCCCCCCCCCCC(=O)OC[CH](CO)OC(=O)CCCCCCCCCC=CCCCCCC
FormulaC37 H70 O5
Name(2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate
ChEMBL
DrugBank
ZINCZINC000040164687
PDB chain8ijr Chain D 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]
PDB8ijr Cryo-EM structure of human sphingomyelin synthase and its mechanistic implications for sphingomyelin synthesis.
Resolution3.29 Å
Binding residue
(original residue number in PDB)		F163 M170 L232 M285 D295 H301 V304
Binding residue
(residue number reindexed from 1)		F20 M27 L89 M142 D152 H158 V161
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.8.-
Gene Ontology
Molecular Function
GO:0002950 ceramide phosphoethanolamine synthase activity
GO:0003674 molecular_function
GO:0016740 transferase activity
GO:0016780 phosphotransferase activity, for other substituted phosphate groups
GO:0033188 sphingomyelin synthase activity
GO:0047493 ceramide cholinephosphotransferase activity
Biological Process
GO:0006665 sphingolipid metabolic process
GO:0006686 sphingomyelin biosynthetic process
GO:0046513 ceramide biosynthetic process
GO:1905373 ceramide phosphoethanolamine biosynthetic process
GO:2000303 regulation of ceramide biosynthetic process
Cellular Component
GO:0000139 Golgi membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ijr, PDBe:8ijr, PDBj:8ijr
PDBsum8ijr
PubMed38388831
UniProtQ96LT4|SAMD8_HUMAN Sphingomyelin synthase-related protein 1 (Gene Name=SAMD8)

[Back to BioLiP]