Structure of PDB 8uo8 Chain A Binding Site BS02

Receptor Information
>8uo8 Chain A (length=574) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEEQLAHQYETIMDECGHGRFQWILFFVLGLALMADGVEVFVVSFALPSA
EKDMCLSSSKKGMLGMIVYLGMMAGAFILGGLADKLGRKRVLSMSLAVNA
SFASLSSFVQGYGAFLFCRLISGIGIGGALPIVFAYFSEFLSREKRGEHL
SWLGIFWMTGGLYASAMAWSIIPHYGWGFSMGTNYHFHSWRVFVIVCALP
CTVSMVALKFMPESPRFLLEMGKHDEAWMILKQVHDTNMRAKGTPEKVFT
VSNIKTPFKTIFKQVWDNALYCVMGPYRMNTLILAVVWFAMAFSYYGLTV
WFPDMIRYFQDEEYKSKMKVFFGEHVYGATINFTMENQIHQHGKLVNDKF
TRMYFKHVLFEDTFFDECYFEDVTSTDTYFKNCTIESTIFYNTDLYEHKF
INCRFINSTFLEQKEGCHMDLEQDNDFLIYLVSFLGSLSVLPGNIISALL
MDRIGRLKMIGGSMLISAVCCFFLFFGNSESAMIGWQCLFCGTSIAAWNA
LDVITVELYPTNQRATAFGILNGLCKFGAILGNTIFASFVGITKVVPILL
AAASLVGGGLIALRLPETREQVLM
Ligand information
Ligand IDPS1
InChIInChI=1S/C26H50NO10P/c1-3-5-7-9-11-13-15-17-24(28)34-19-22(20-35-38(32,33)36-21-23(27)26(30)31)37-25(29)18-16-14-12-10-8-6-4-2/h22-23H,3-21,27H2,1-2H3,(H,30,31)(H,32,33)/p-1/t22-,23+/m1/s1
InChIKeyLRIPXDCMGANCAE-PKTZIBPZSA-M
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCC(=O)OC[C@H](CO[P]([O-])(=O)OC[C@H](N)C(O)=O)OC(=O)CCCCCCCCC
ACDLabs 10.04O=C(OCC(OC(=O)CCCCCCCCC)COP([O-])(=O)OCC(N)C(=O)O)CCCCCCCCC
OpenEye OEToolkits 1.5.0CCCCCCCCCC(=O)OCC(COP(=O)([O-])OCC(C(=O)O)N)OC(=O)CCCCCCCCC
CACTVS 3.341CCCCCCCCCC(=O)OC[CH](CO[P]([O-])(=O)OC[CH](N)C(O)=O)OC(=O)CCCCCCCCC
OpenEye OEToolkits 1.5.0CCCCCCCCCC(=O)OC[C@H](CO[P@](=O)([O-])OC[C@@H](C(=O)O)N)OC(=O)CCCCCCCCC
FormulaC26 H49 N O10 P
Name1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]
ChEMBL
DrugBank
ZINC
PDB chain8uo8 Chain A Residue 705 [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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PDB8uo8 Structure of synaptic vesicle protein 2B with padsevonil
Resolution3.2 Å
Binding residue
(original residue number in PDB)
H104 G105 W109 F113
Binding residue
(residue number reindexed from 1)
H18 G19 W23 F27
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
Biological Process
GO:0006836 neurotransmitter transport
GO:0099509 regulation of presynaptic cytosolic calcium ion concentration
GO:2000300 regulation of synaptic vesicle exocytosis
Cellular Component
GO:0001669 acrosomal vesicle
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0045202 synapse

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8uo8, PDBe:8uo8, PDBj:8uo8
PDBsum8uo8
PubMed38898101
UniProtQ7L1I2|SV2B_HUMAN Synaptic vesicle glycoprotein 2B (Gene Name=SV2B)

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