Structure of PDB 8ss3 Chain A Binding Site BS04

Receptor Information
>8ss3 Chain A (length=596) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYK
LTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDF
SKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLF
LVSRFSPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLI
IISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRR
SKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEY
IEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVLDK
LKNKWWYDKGECGAKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKS
RAEAGRKALTLLSSVFAVCGLGLLGIAVSTDYWLYLEEGIILPQNQSTEV
KMSLHSGLWRVCFLAGEERGRCFTIEYVMVNVLKMIRSATPFPLVSLFFM
FIGFILSNIGHIRPHRTILAFVSGIFFILSGLSLVVGLVLYISSINDEML
NRTKDAETYFNYKYGWSFAFAAISFLLTESAGVMSVYLFMKRYTAE
Ligand information
Ligand IDAJP
InChIInChI=1S/C56H92O29/c1-19-7-10-56(75-17-19)20(2)31-45(85-56)37(67)32-22-6-5-21-11-26(24(61)12-55(21,4)23(22)8-9-54(31,32)3)76-50-42(72)39(69)44(30(16-60)80-50)81-53-48(47(36(66)29(15-59)79-53)83-49-40(70)33(63)25(62)18-74-49)84-52-43(73)46(35(65)28(14-58)78-52)82-51-41(71)38(68)34(64)27(13-57)77-51/h19-53,57-73H,5-18H2,1-4H3/t19-,20+,21+,22-,23+,24-,25-,26-,27-,28-,29-,30-,31+,32-,33+,34-,35+,36-,37+,38+,39-,40-,41-,42-,43-,44+,45-,46+,47+,48-,49+,50-,51+,52+,53+,54-,55+,56-/m1/s1
InChIKeyUVYVLBIGDKGWPX-KUAJCENISA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CC1C2C(OC31CCC(C)CO3)C(O)C1C3CCC4CC(OC5OC(CO)C(OC6OC(CO)C(O)C(OC7OCC(O)C(O)C7O)C6OC6OC(CO)C(O)C(OC7OC(CO)C(O)C(O)C7O)C6O)C(O)C5O)C(O)CC4(C)C3CCC21C
CACTVS 3.385C[CH]1CC[C]2(OC1)O[CH]3[CH](O)[CH]4[CH]5CC[CH]6C[CH](O[CH]7O[CH](CO)[CH](O[CH]8O[CH](CO)[CH](O)[CH](O[CH]9OC[CH](O)[CH](O)[CH]9O)[CH]8O[CH]%10O[CH](CO)[CH](O)[CH](O[CH]%11O[CH](CO)[CH](O)[CH](O)[CH]%11O)[CH]%10O)[CH](O)[CH]7O)[CH](O)C[C]6(C)[CH]5CC[C]4(C)[CH]3[CH]2C
CACTVS 3.385C[C@@H]1CC[C@@]2(OC1)O[C@H]3[C@@H](O)[C@H]4[C@@H]5CC[C@H]6C[C@@H](O[C@@H]7O[C@H](CO)[C@H](O[C@@H]8O[C@H](CO)[C@@H](O)[C@H](O[C@@H]9OC[C@@H](O)[C@H](O)[C@H]9O)[C@H]8O[C@@H]%10O[C@H](CO)[C@H](O)[C@H](O[C@@H]%11O[C@H](CO)[C@@H](O)[C@H](O)[C@H]%11O)[C@H]%10O)[C@H](O)[C@H]7O)[C@H](O)C[C@]6(C)[C@H]5CC[C@]4(C)[C@H]3[C@@H]2C
OpenEye OEToolkits 2.0.7CC1CCC2(C(C3C(O2)C(C4C3(CCC5C4CCC6C5(CC(C(C6)OC7C(C(C(C(O7)CO)OC8C(C(C(C(O8)CO)O)OC9C(C(C(CO9)O)O)O)OC2C(C(C(C(O2)CO)O)OC2C(C(C(C(O2)CO)O)O)O)O)O)O)O)C)C)O)C)OC1
OpenEye OEToolkits 2.0.7C[C@@H]1CC[C@@]2([C@H]([C@H]3[C@@H](O2)[C@H]([C@@H]4[C@@]3(CC[C@H]5[C@H]4CC[C@@H]6[C@@]5(C[C@H]([C@@H](C6)O[C@H]7[C@@H]([C@H]([C@H]([C@H](O7)CO)O[C@H]8[C@@H]([C@H]([C@@H]([C@H](O8)CO)O)O[C@H]9[C@@H]([C@H]([C@@H](CO9)O)O)O)O[C@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O)O)O)C)C)O)C)OC1
FormulaC56 H92 O29
NameDigitonin
ChEMBL
DrugBank
ZINC
PDB chain8ss3 Chain A Residue 1111 [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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PDB8ss3 Modulation of GluA2-gamma 5 synaptic complex desensitization, polyamine block and antiepileptic perampanel inhibition by auxiliary subunit cornichon-2.
Resolution3.21 Å
Binding residue
(original residue number in PDB)		G853 S857
Binding residue
(residue number reindexed from 1)		G425 S429
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000149 SNARE binding
GO:0001540 amyloid-beta binding
GO:0004970 glutamate-gated receptor activity
GO:0004971 AMPA glutamate receptor activity
GO:0005230 extracellular ligand-gated monoatomic ion channel activity
GO:0005234 extracellularly glutamate-gated ion channel activity
GO:0005515 protein binding
GO:0008092 cytoskeletal protein binding
GO:0015276 ligand-gated monoatomic ion channel activity
GO:0015277 kainate selective glutamate receptor activity
GO:0019865 immunoglobulin binding
GO:0019901 protein kinase binding
GO:0022849 glutamate-gated calcium ion channel activity
GO:0030165 PDZ domain binding
GO:0035254 glutamate receptor binding
GO:0035255 ionotropic glutamate receptor binding
GO:0038023 signaling receptor activity
GO:0042802 identical protein binding
GO:0044877 protein-containing complex binding
GO:0097110 scaffold protein binding
GO:0099094 ligand-gated monoatomic cation channel activity
GO:0099507 ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential
GO:1904315 transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential
Biological Process
GO:0001919 regulation of receptor recycling
GO:0006816 calcium ion transport
GO:0007268 chemical synaptic transmission
GO:0010226 response to lithium ion
GO:0019722 calcium-mediated signaling
GO:0021987 cerebral cortex development
GO:0031623 receptor internalization
GO:0034220 monoatomic ion transmembrane transport
GO:0035235 ionotropic glutamate receptor signaling pathway
GO:0035249 synaptic transmission, glutamatergic
GO:0045184 establishment of protein localization
GO:0050804 modulation of chemical synaptic transmission
GO:0050806 positive regulation of synaptic transmission
GO:0051262 protein tetramerization
GO:0051966 regulation of synaptic transmission, glutamatergic
GO:0060078 regulation of postsynaptic membrane potential
GO:0060079 excitatory postsynaptic potential
GO:0060992 response to fungicide
GO:0098655 monoatomic cation transmembrane transport
GO:0099505 regulation of presynaptic membrane potential
GO:1905430 cellular response to glycine
GO:1990416 cellular response to brain-derived neurotrophic factor stimulus
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0008328 ionotropic glutamate receptor complex
GO:0009986 cell surface
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030424 axon
GO:0030425 dendrite
GO:0030426 growth cone
GO:0030672 synaptic vesicle membrane
GO:0032279 asymmetric synapse
GO:0032281 AMPA glutamate receptor complex
GO:0032590 dendrite membrane
GO:0032839 dendrite cytoplasm
GO:0032991 protein-containing complex
GO:0036477 somatodendritic compartment
GO:0042734 presynaptic membrane
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0043195 terminal bouton
GO:0043197 dendritic spine
GO:0043198 dendritic shaft
GO:0043204 perikaryon
GO:0044326 dendritic spine neck
GO:0044327 dendritic spine head
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0048787 presynaptic active zone membrane
GO:0097060 synaptic membrane
GO:0098685 Schaffer collateral - CA1 synapse
GO:0098793 presynapse
GO:0098839 postsynaptic density membrane
GO:0098978 glutamatergic synapse
GO:0099544 perisynaptic space
GO:0106033 spine synapse

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ss3, PDBe:8ss3, PDBj:8ss3
PDBsum8ss3
PubMed37653241
UniProtP19491|GRIA2_RAT Glutamate receptor 2 (Gene Name=Gria2);
Q8VHW8

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