Structure of PDB 4u5d Chain B Binding Site BS01

Receptor Information

>4u5d Chain B (length=738) Species: 10116 (Rattus norvegicus)

NSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVT
NAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPF
VIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQ
VTAINVGNINNDKKDETYRSLFQDLELKGERRVILDCERDKVNDIVDQVI
TIGKHVKGYHYIIANLGFTDGDLLKIQFGGAEVSGFQIVDYDDSLVSKFI
ERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR
GNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTIN
IMELKTNGPRKIGYWSEVDKMVVTLTESGDLEQKTVVVTTILESPYVMMK
KNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKI
WDGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQK
SKPGVFSFLDPLAYEIWMAIVFAYILVSVVLFLSARIVAGVWWFFTLIII
SSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSK
IAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIE
QRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVLDKLK
NKWWYDKGECGSLSNVAGVFYILVGGLGLAMLVALIEF

Ligand information

• Ligand ID: FWF
• InChI: InChI=1S/C24H36N2O4S2/c1-17(2)31(27,28)25-15-19(5)21-7-11-23(12-8-21)24-13-9-22(10-14-24)20(6)16-26-32(29,30)18(3)4/h7-14,17-20,25-26H,15-16H2,1-6H3/t19-,20-/m0/s1
• InChIKey: HGLQSTHVRKGLQP-PMACEKPBSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: CC(C)S(=O)(=O)NCC(C)c1ccc(cc1)c2ccc(cc2)C(C)CNS(=O)(=O)C(C)C
  CACTVS 3.385: CC(C)[S](=O)(=O)NC[CH](C)c1ccc(cc1)c2ccc(cc2)[CH](C)CN[S](=O)(=O)C(C)C
  ACDLabs 12.01: O=S(=O)(NCC(c2ccc(c1ccc(cc1)C(CNS(=O)(=O)C(C)C)C)cc2)C)C(C)C
  OpenEye OEToolkits 1.9.2: C[C@@H](CNS(=O)(=O)C(C)C)c1ccc(cc1)c2ccc(cc2)[C@@H](C)CNS(=O)(=O)C(C)C
  CACTVS 3.385: CC(C)[S](=O)(=O)NC[C@H](C)c1ccc(cc1)c2ccc(cc2)[C@@H](C)CN[S](=O)(=O)C(C)C
• Formula: C24 H36 N2 O4 S2
• Name: N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide
• ZINC: ZINC000098208908
• PDB chain: 4u5d Chain B Residue 903

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4u5d X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism.
• Resolution: 3.5757 Å
• Binding residue (original residue number in PDB): P494 M496 S497 S729 L751 S754
• Binding residue (residue number reindexed from 1): P485 M487 S488 S666 L688 S691
• 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:4u5d, PDBe:4u5d, PDBj:4u5d
• PDBsum: 4u5d
• PubMed: 25103405
• UniProt: P19491|GRIA2_RAT Glutamate receptor 2 (Gene Name=Gria2)