Structure of PDB 6ruq Chain B Binding Site BS01

Receptor Information

>6ruq Chain B (length=781) Species: 10116 (Rattus norvegicus)

NSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVT
NAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPF
VIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQ
VTAINVGNINNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVI
TIGKHVKGYHYIIANLGFTDGDLLKIQFGGAEVSGFQIVDYDDSLVSKFI
ERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR
GNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTIN
IMELKTNGPRKIGYWSEVDKMVLTEDDTSGLEQKTVVVTTILESPYVMMK
ANHAALAGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKI
WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQK
SKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRAIFQSAWFSLGAFM
QQGADISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIES
AEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRT
TAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIA
TPKGSSLGTPVNLAVLKLSEQGLLDKLKNKWWYDKGECGAKDSGSKEKTS
ALSLSNVAGVFYILVGGLGLAMLVALIEFCY

Ligand information

• Ligand ID: GYK
• InChI: InChI=1S/C19H20N4O3/c1-11-7-13-8-16-17(26-10-25-16)9-15(13)18(22-23(11)19(24)21-2)12-3-5-14(20)6-4-12/h3-6,8-9,11H,7,10,20H2,1-2H3,(H,21,24)/t11-/m1/s1
• InChIKey: SMGACXZFVXKEAX-LLVKDONJSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC1Cc2cc3c(cc2C(=NN1C(=O)NC)c4ccc(cc4)N)OCO3
  CACTVS 3.385: CNC(=O)N1N=C(c2ccc(N)cc2)c3cc4OCOc4cc3C[C@H]1C
  ACDLabs 12.01: CC2Cc1cc4c(cc1C(=NN2C(=O)NC)c3ccc(cc3)N)OCO4
  OpenEye OEToolkits 2.0.6: C[C@@H]1Cc2cc3c(cc2C(=NN1C(=O)NC)c4ccc(cc4)N)OCO3
  CACTVS 3.385: CNC(=O)N1N=C(c2ccc(N)cc2)c3cc4OCOc4cc3C[CH]1C
• Formula: C19 H20 N4 O3
• Name: (8R)-5-(4-aminophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide
• ChEMBL: CHEMBL411664
• ZINC: ZINC000000598361
• PDB chain: 6ruq Chain B Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ruq Binding of a negative allosteric modulator and competitive antagonist can occur simultaneously at the ionotropic glutamate receptor GluA2.
• Resolution: 4.65 Å
• Binding residue (original residue number in PDB): F517 P520 Y616 L620 F623 S788 N791
• Binding residue (residue number reindexed from 1): F508 P511 Y581 L585 F588 S753 N756
• Annotation score: 1

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

External links

• PDB: RCSB:6ruq, PDBe:6ruq, PDBj:6ruq
• PDBsum: 6ruq
• PubMed: 32543078
• UniProt: P19491|GRIA2_RAT Glutamate receptor 2 (Gene Name=Gria2)