Structure of PDB 5vyp Chain T Binding Site BS02

Receptor Information
>5vyp Chain T (length=48) Species: 200320 (Nicotiana suaveolens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKDCKRESNTFPGICITKPPCRKACIREKFTDGHCSKILRRCLCTKPC
Ligand information
Ligand IDPIO
InChIInChI=1S/C25H49O19P3/c1-3-5-7-9-11-13-18(26)39-15-17(41-19(27)14-12-10-8-6-4-2)16-40-47(37,38)44-23-20(28)21(29)24(42-45(31,32)33)25(22(23)30)43-46(34,35)36/h17,20-25,28-30H,3-16H2,1-2H3,(H,37,38)(H2,31,32,33)(H2,34,35,36)/t17-,20-,21+,22+,23-,24-,25-/m1/s1
InChIKeyXLNCEHRXXWQMPK-MJUMVPIBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCC(=O)OC[C@H](CO[P](O)(=O)O[C@@H]1[C@H](O)[C@H](O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O)OC(=O)CCCCCCC
CACTVS 3.385CCCCCCCC(=O)OC[CH](CO[P](O)(=O)O[CH]1[CH](O)[CH](O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]1O)OC(=O)CCCCCCC
OpenEye OEToolkits 1.9.2CCCCCCCC(=O)OCC(COP(=O)(O)OC1C(C(C(C(C1O)OP(=O)(O)O)OP(=O)(O)O)O)O)OC(=O)CCCCCCC
OpenEye OEToolkits 1.9.2CCCCCCCC(=O)OC[C@H](COP(=O)(O)O[C@@H]1[C@@H]([C@@H]([C@H]([C@@H]([C@H]1O)OP(=O)(O)O)OP(=O)(O)O)O)O)OC(=O)CCCCCCC
ACDLabs 12.01O=C(OCC(OC(=O)CCCCCCC)COP(=O)(O)OC1C(O)C(O)C(OP(=O)(O)O)C(OP(=O)(O)O)C1O)CCCCCCC
FormulaC25 H49 O19 P3
Name[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate;
dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate
ChEMBL
DrugBank
ZINCZINC000097972490
PDB chain5vyp Chain T Residue 101 [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]
PDB5vyp Structure of the defensin NsD7 in complex with PIP2 reveals that defensin : lipid oligomer topologies are dependent on lipid type.
Resolution2.6 Å
Binding residue
(original residue number in PDB)
K1 K4 H33 S35 K36 I37 L38 R40
Binding residue
(residue number reindexed from 1)
K2 K5 H34 S36 K37 I38 L39 R41
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008289 lipid binding
GO:0070300 phosphatidic acid binding
Biological Process
GO:0006952 defense response
GO:0031640 killing of cells of another organism
Cellular Component
GO:0005773 vacuole

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:5vyp, PDBe:5vyp, PDBj:5vyp
PDBsum5vyp
PubMed28741756
UniProtC0HK49|DEF_NICSU Defensin NsD7

[Back to BioLiP]