Structure of PDB 8qbd Chain N Binding Site BS02

Receptor Information
>8qbd Chain N (length=271) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHRTYSLRNSRAPTASQLQNPPPPPSTTKGRFFGKGGLAYSFRRSAAGAF
GPELSRKLSQLVKIEKNVLRSMELTANERRDAAKQLSIWGLENDDDVSDI
TDKLGVLIYEVSELDDQFIDRYDQYRLTLKSIRDIEGSVQPSRDRKDKIT
DKIAYLKYKDPQSPKIEVLEQELVRAEAESLVAEAQLSNITRSKLRAAFN
YQFDSIIEHSEKIALIAGYGKALLELLDDSPVTPGETRPAYDGYEASKQI
IIDAESALNEWTLDSAQVKPT
Ligand information
Ligand IDP5S
InChIInChI=1S/C42H82NO10P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-40(44)50-35-38(36-51-54(48,49)52-37-39(43)42(46)47)53-41(45)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h38-39H,3-37,43H2,1-2H3,(H,46,47)(H,48,49)/t38-,39+/m1/s1
InChIKeyTZCPCKNHXULUIY-RGULYWFUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OC[CH](N)C(O)=O)OC(=O)CCCCCCCCCCCCCCCCC
CACTVS 3.370CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P](O)(=O)OC[C@H](N)C(O)=O)OC(=O)CCCCCCCCCCCCCCCCC
ACDLabs 12.01O=C(OC(COP(=O)(OCC(C(=O)O)N)O)COC(=O)CCCCCCCCCCCCCCCCC)CCCCCCCCCCCCCCCCC
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC(C(=O)O)N)OC(=O)CCCCCCCCCCCCCCCCC
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC[C@@H](C(=O)O)N)OC(=O)CCCCCCCCCCCCCCCCC
FormulaC42 H82 N O10 P
NameO-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine;
phosphatidyl serine
ChEMBLCHEMBL4297669
DrugBankDB00144
ZINCZINC000085588270
PDB chain8qbd Chain N Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8qbd Real-space refinement in PHENIX for cryo-EM and crystallography.
Resolution3.61 Å
Binding residue
(original residue number in PDB)		A39 R43 K63 K66 R70
Binding residue
(residue number reindexed from 1)		A39 R43 K63 K66 R70
Annotation score4
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008289 lipid binding
Biological Process
GO:0006897 endocytosis
GO:0008104 protein localization
GO:0070941 eisosome assembly
GO:0097446 protein localization to eisosome filament
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005811 lipid droplet
GO:0005886 plasma membrane
GO:0032126 eisosome
GO:0036286 eisosome filament
GO:0071944 cell periphery

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8qbd, PDBe:8qbd, PDBj:8qbd
PDBsum8qbd
PubMed39048819
UniProtP53252|PIL1_YEAST Sphingolipid long chain base-responsive protein PIL1 (Gene Name=PIL1)

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