Structure of PDB 8uo9 Chain A Binding Site BS01

Receptor Information
>8uo9 Chain A (length=555) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EREELAQQYEAILRECGHGRFQWTLYFVLGLALMADGVEVFVVGFVLPSA
EKDMLGLIVYLGMMVGAFLWGGLADRLGRRQCLLISLSVNSVFAFFSSFV
QGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEHLSWLCMFWMI
GGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALT
TQPESPRFFLENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIYQRWG
VRALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDM
IRHLQAVDYASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRL
KSVSFEDSLFEECYFEDVTSSNTFFRNCTFINTVFYNTDLFEYKFVNSRL
INSTFLHNKEAYMVYFVSFLGTLAVLPGNIVSALLMDKIGRLRMLAGSSV
MSCVSCFFLSFGNSESAMIALLCLFGGVSIASWNALDVLTVELYPSDKRT
TAFGFLNALCKLAAVLGISIFTSFVGITKAAPILFASAALALGSSLALKL
PETRG
Ligand information
Ligand IDX49
InChIInChI=1S/C16H18F6N4O2S/c1-28-8-11-24-26-10(13(16(20,21)22)23-14(26)29-11)7-25-6-9(5-12(25)27)3-2-4-15(17,18)19/h9H,2-8H2,1H3/t9-/m1/s1
InChIKeyRBBCVRVBYUAJOO-SECBINFHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COCc1nn2c(c(nc2s1)C(F)(F)F)CN3C[C@@H](CC3=O)CCCC(F)(F)F
ACDLabs 12.01FC(F)(F)CCCC1CC(=O)N(C1)Cc1c(nc2sc(COC)nn12)C(F)(F)F
CACTVS 3.385COCc1sc2nc(c(CN3C[C@H](CCCC(F)(F)F)CC3=O)n2n1)C(F)(F)F
OpenEye OEToolkits 2.0.7COCc1nn2c(c(nc2s1)C(F)(F)F)CN3CC(CC3=O)CCCC(F)(F)F
CACTVS 3.385COCc1sc2nc(c(CN3C[CH](CCCC(F)(F)F)CC3=O)n2n1)C(F)(F)F
FormulaC16 H18 F6 N4 O2 S
Name(4R)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}-4-(4,4,4-trifluorobutyl)pyrrolidin-2-one
ChEMBL
DrugBank
ZINC
PDB chain8uo9 Chain A Residue 801 [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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PDB8uo9 Structure of synaptic vesicle protein 2A in complex with a nanobody
Resolution3.3 Å
Binding residue
(original residue number in PDB)		C297 W300 W454 Y461 V608 I663 W666 D670 F686 N690 C693 K694
Binding residue
(residue number reindexed from 1)		C145 W148 W283 Y290 V425 I480 W483 D487 F503 N507 C510 K511
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0019901 protein kinase binding
Biological Process
GO:0006836 neurotransmitter transport
GO:0006874 intracellular calcium ion homeostasis
GO:0014052 regulation of gamma-aminobutyric acid secretion
GO:0016082 synaptic vesicle priming
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0030425 dendrite
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031594 neuromuscular junction
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0045202 synapse
GO:0048786 presynaptic active zone
GO:0098793 presynapse
GO:0098978 glutamatergic synapse
GO:0098982 GABA-ergic synapse

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8uo9, PDBe:8uo9, PDBj:8uo9
PDBsum8uo9
PubMed38898101
UniProtQ7L0J3|SV2A_HUMAN Synaptic vesicle glycoprotein 2A (Gene Name=SV2A)

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