Structure of PDB 3kyq Chain A Binding Site BS01

Receptor Information
>3kyq Chain A (length=193) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LMKLYSLSVFYKGEPKAVLLKAAYDVSSFSFFQRSSVQEFMTFTSQLIVE
RSAKGSRASVKEQEYLCHVYVRSDSLAGVVIADSEYPSRVAFTLLEKVLD
EFSKQVDRIDWPVGSPATIHYTALDGHLSRYQNPREADPMSKVQAELDET
KIILHNTMESLLERGEKLDDLVSKSEVLGTQSKAFYKTARKQN
Ligand information
Ligand IDDPV
InChIInChI=1S/C17H38NO4P/c1-5-6-7-8-9-10-11-12-13-14-16-21-23(19,20)22-17-15-18(2,3)4/h5-17H2,1-4H3
InChIKeyQBHFVMDLPTZDOI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCCCCCCCCCCO[P@](=O)([O-])OCC[N+](C)(C)C
OpenEye OEToolkits 1.7.0CCCCCCCCCCCCOP(=O)([O-])OCC[N+](C)(C)C
CACTVS 3.352CCCCCCCCCCCCO[P]([O-])(=O)OCC[N+](C)(C)C
FormulaC17 H38 N O4 P
Namedodecyl 2-(trimethylammonio)ethyl phosphate;
dodecylphosphocholine
ChEMBLCHEMBL229565
DrugBank
ZINC
PDB chain3kyq Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kyq Lipid-Induced Conformational Switch Controls Fusion Activity of Longin Domain SNARE Ykt6
Resolution2.443 Å
Binding residue
(original residue number in PDB)		S27 F28 Q32 T43 Y64
Binding residue
(residue number reindexed from 1)		S28 F29 Q33 T44 Y65
Annotation score1
Binding affinityMOAD: Kd=61uM
PDBbind-CN: -logKd/Ki=4.22,Kd=60uM
Enzymatic activity
Enzyme Commision number 2.3.1.-
Gene Ontology
Molecular Function
GO:0005484 SNAP receptor activity
GO:0016740 transferase activity
GO:0019706 protein-cysteine S-palmitoyltransferase activity
Biological Process
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport
GO:0006903 vesicle targeting
GO:0006904 vesicle docking involved in exocytosis
GO:0008150 biological_process
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0042147 retrograde transport, endosome to Golgi
GO:0061025 membrane fusion
Cellular Component
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031201 SNARE complex
GO:0031410 cytoplasmic vesicle
GO:0043025 neuronal cell body
GO:0097440 apical dendrite
GO:0097441 basal dendrite

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3kyq, PDBe:3kyq, PDBj:3kyq
PDBsum3kyq
PubMed20159557
UniProtQ5EGY4|YKT6_RAT Synaptobrevin homolog YKT6 (Gene Name=Ykt6)

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