Structure of PDB 5wen Chain C Binding Site BS01

Receptor Information
>5wen Chain C (length=962) Species: 10090,10116 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVT
NAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPF
VIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQ
VTAINVGNINNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVI
TIGKHVKGYHYIIANLGFTDGDLLKIQFGGAEVSGFQIVDYDDSLVSKFI
ERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR
GNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTIN
IMELKTNGPRKIGYWSEVDKMVLTEDDTSGLEQKTVVVTTILESPYVMMK
KNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKI
WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQK
SKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSIFNSLWFSLGAFMQQ
GCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAE
DLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTA
EGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATP
KGSSLGTPVNLAVLKLSEQGVLDKLKNKWWYDKGECGAKDSGSKEKTSAL
SLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAKTSRRGRALLAVALNLL
ALLFATTAFLTTYWCQGTQRVPFQLRRFHTGIWYSCEEGEKCRSFIDLAP
ASEKGVLWLSVVSEVLYILLLVVGFSLMCLELLHSSDGLKLNAFAAVFTV
LSGLLGMVAHMMYTQVFQVTVSLGPEDWRPHSWDYGWSFCLAWGSFTCCM
AASVTTLNSYTK
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 chain5wen Chain C Residue 1301 [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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PDB5wen Channel opening and gating mechanism in AMPA-subtype glutamate receptors.
Resolution6.8 Å
Binding residue
(original residue number in PDB)		Y127 Y128 Q129 K216 G217 Y218 E241 L382 V468 Y469 G470 P737 S740 S741
Binding residue
(residue number reindexed from 1)		Y118 Y119 Q120 K207 G208 Y209 E232 L373 V459 Y460 G461 P700 S703 S704
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:0005216 monoatomic ion channel 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:0006811 monoatomic 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
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Biological Process
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Cellular Component
External links
PDB RCSB:5wen, PDBe:5wen, PDBj:5wen
PDBsum5wen
PubMed28737760
UniProtD3Z7H4;
P19491|GRIA2_RAT Glutamate receptor 2 (Gene Name=Gria2)

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