Structure of PDB 6i3y Chain F Binding Site BS01

Receptor Information
>6i3y Chain F (length=182) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHHHHHHSDQMVKYFLGQSVLRSSWDQVFAAFWQRYPNPYSKHVLTEDIV
HREVTPDQKLLSRRLLTVTNRMPRWAERLFPANVAHSVYVLEDSIVDPQN
QTMTTFTWNINHARLMVVEERSVYSVNSDNSGWTEIRREAWVSSSLFGVS
RAVQEFGLARFKSNVTKTMKGFEYILAKLQGE
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 chain6i3y Chain F Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6i3y Structural determinants of lipid specificity within Ups/PRELI lipid transfer proteins.
Resolution2.98 Å
Binding residue
(original residue number in PDB)
Y37 Y41 H44 V69 T70 N71 M73 V91 N110 H113 V119
Binding residue
(residue number reindexed from 1)
Y36 Y40 H43 V68 T69 N70 M72 V90 N109 H112 V118
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Cellular Component
GO:0005758 mitochondrial intermembrane space

View graph for
Cellular Component
External links
PDB RCSB:6i3y, PDBe:6i3y, PDBj:6i3y
PDBsum6i3y
PubMed30850607
UniProtQ9Y255|PRLD1_HUMAN PRELI domain-containing protein 1, mitochondrial (Gene Name=PRELID1)

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