Structure of PDB 8gc3 Chain A Binding Site BS01

Receptor Information
>8gc3 Chain A (length=742) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKI
NLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTR
WKHQVSDNKDSFYVSLYPDFSSLSRAILDLVQFFKWKTVTVVYDDSTGLI
RLQELIKAPSRYNLRLKIRQLPADTKDAKPLLKEMKRGKEFHVIFDCSHE
MAAGILKQALAMGMMTEYYHYIFTTLDLFALDVEPYRYSGVNMTGFRILN
TENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVA
VQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGL
RTDFDLDVISLKEEGLEKIGTWDPASGLNMTESQKGKPANITDSLSNRSL
IVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLV
EDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPF
MTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLAYLGVSVVLFVILS
TRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEY
GAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSD
YAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAI
LQLQEEGKLHMMKEKWWRGVQNIGGIFIVLAAGLVLSVFVAV
Ligand information
Ligand IDDOQ
InChIInChI=1S/C15H21NO6/c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)22)10(11)6-12(17)18/h3-5,9-11,13,16H,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/b5-3+,8-4-/t9-,10+,11-,13+/m1/s1
InChIKeyVZFRNCSOCOPNDB-AOKDLOFSSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(/C=C/C=C(\C1C(C(C(=O)O)NC1)CC(=O)O)C)C
OpenEye OEToolkits 1.5.0CC(C=CC=C(C)C1CNC(C1CC(=O)O)C(=O)O)C(=O)O
OpenEye OEToolkits 1.5.0C[C@H](\C=C\C=C(\C)/[C@H]1CN[C@@H]([C@H]1CC(=O)O)C(=O)O)C(=O)O
CACTVS 3.341C[CH](C=CC=C(C)[CH]1CN[CH]([CH]1CC(O)=O)C(O)=O)C(O)=O
CACTVS 3.341C[C@H](\C=C\C=C(\C)[C@H]1CN[C@@H]([C@H]1CC(O)=O)C(O)=O)C(O)=O
FormulaC15 H21 N O6
Name(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID;
(2S,3S,4S)-3-CARBOXYMETHYL-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-HEXA-1,3-DIENYL]-PYRROLIDINE-2-CARBOXYLIC ACID;
DOMOIC ACID
ChEMBLCHEMBL1232313
DrugBankDB02852
ZINCZINC000003995581
PDB chain8gc3 Chain A Residue 1002 [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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PDB8gc3 Structural basis for kainate receptor activation by a partial agonist
Resolution3.8 Å
Binding residue
(original residue number in PDB)		K487 Y488 P516 L517 V685 E686 D687 G688 N721 E738
Binding residue
(residue number reindexed from 1)		K454 Y455 P483 L484 V603 E604 D605 G606 N639 E656
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000149 SNARE binding
GO:0004970 glutamate-gated receptor activity
GO:0005216 monoatomic ion channel activity
GO:0005234 extracellularly glutamate-gated ion channel activity
GO:0005515 protein binding
GO:0008066 glutamate receptor activity
GO:0015276 ligand-gated monoatomic ion channel activity
GO:0015277 kainate selective glutamate receptor activity
GO:0022849 glutamate-gated calcium ion channel activity
GO:0030165 PDZ domain binding
GO:0031624 ubiquitin conjugating enzyme binding
GO:0031625 ubiquitin protein ligase binding
GO:0038023 signaling receptor activity
GO:0042802 identical protein binding
GO:0097110 scaffold protein binding
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:0001662 behavioral fear response
GO:0006811 monoatomic ion transport
GO:0006874 intracellular calcium ion homeostasis
GO:0007268 chemical synaptic transmission
GO:0019228 neuronal action potential
GO:0019722 calcium-mediated signaling
GO:0034220 monoatomic ion transmembrane transport
GO:0035235 ionotropic glutamate receptor signaling pathway
GO:0035249 synaptic transmission, glutamatergic
GO:0042391 regulation of membrane potential
GO:0043113 receptor clustering
GO:0043524 negative regulation of neuron apoptotic process
GO:0043525 positive regulation of neuron apoptotic process
GO:0046328 regulation of JNK cascade
GO:0048169 regulation of long-term neuronal synaptic plasticity
GO:0048172 regulation of short-term neuronal synaptic plasticity
GO:0050804 modulation of chemical synaptic transmission
GO:0050806 positive regulation of synaptic transmission
GO:0051402 neuron apoptotic process
GO:0051967 negative regulation of synaptic transmission, glutamatergic
GO:0060079 excitatory postsynaptic potential
GO:0060080 inhibitory postsynaptic potential
GO:0098815 modulation of excitatory postsynaptic potential
GO:0099171 presynaptic modulation of chemical synaptic transmission
GO:0099505 regulation of presynaptic membrane potential
GO:0120169 detection of cold stimulus involved in thermoception
Cellular Component
GO:0005886 plasma membrane
GO:0008328 ionotropic glutamate receptor complex
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030424 axon
GO:0030425 dendrite
GO:0032839 dendrite cytoplasm
GO:0032983 kainate selective glutamate receptor complex
GO:0042734 presynaptic membrane
GO:0043025 neuronal cell body
GO:0043195 terminal bouton
GO:0043204 perikaryon
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0097471 mossy fiber rosette
GO:0098686 hippocampal mossy fiber to CA3 synapse
GO:0098839 postsynaptic density membrane
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8gc3, PDBe:8gc3, PDBj:8gc3
PDBsum8gc3
PubMed
UniProtP42260|GRIK2_RAT Glutamate receptor ionotropic, kainate 2 (Gene Name=Grik2)

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