Structure of PDB 6dm1 Chain D Binding Site BS03

Receptor Information

>6dm1 Chain D (length=985) Species: 9606,10116 [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
SKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYQSSESTNEFG
IFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAA
FLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWT
YMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMK
VGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVLDKLKNKWWYDKGE
CGAKDSGSKEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRLFD
RGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKVMTHSGLWRTCC
LEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMG
GLCIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGKKNSYS
YGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLTG

Ligand information

Ligand ID

CYZ

InChI

InChI=1S/C14H16ClN3O4S2/c15-10-5-11-13(6-12(10)23(16,19)20)24(21,22)18-14(17-11)9-4-7-1-2-8(9)3-7/h1-2,5-9,14,17-18H,3-4H2,(H2,16,19,20)/t7-,8+,9-,14-/m0/s1

InChIKey

BOCUKUHCLICSIY-KSCJFIISSA-N

SMILES

Software	SMILES
ACDLabs 10.04	O=S(=O)(c1c(Cl)cc2c(c1)S(=O)(=O)NC(N2)C4C3C=CC(C3)C4)N
CACTVS 3.341	N[S](=O)(=O)c1cc2c(N[C@@H](N[S]2(=O)=O)[C@H]3C[C@@H]4C[C@H]3C=C4)cc1Cl
CACTVS 3.341	N[S](=O)(=O)c1cc2c(N[CH](N[S]2(=O)=O)[CH]3C[CH]4C[CH]3C=C4)cc1Cl
OpenEye OEToolkits 1.5.0	c1c2c(cc(c1Cl)S(=O)(=O)N)S(=O)(=O)NC(N2)C3CC4CC3C=C4
OpenEye OEToolkits 1.5.0	c1c2c(cc(c1Cl)S(=O)(=O)N)S(=O)(=O)N[C@H](N2)[C@H]3C[C@@H]4C[C@H]3C=C4

Formula

C14 H16 Cl N3 O4 S2

Name

CYCLOTHIAZIDE;
3-BICYCLO[2.2.1]HEPT-5-EN-2-YL-6-CHLORO-3,4- DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE-7-SULFONAMIDE 1,1 DIOXIDE

PDB chain

6dm1 Chain D Residue 1302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6dm1 Mechanisms of Channel Block in Calcium-Permeable AMPA Receptors.
Resolution	4.2 Å
Binding residue (original residue number in PDB)	P494 F495 M496 S497 L759 K763
Binding residue (residue number reindexed from 1)	P485 F486 M487 S488 L737 K741
Annotation score	1

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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Cellular Component

External links

PDB	RCSB:6dm1, PDBe:6dm1, PDBj:6dm1
PDBsum	6dm1
PubMed	30122377
UniProt	P19491\|GRIA2_RAT Glutamate receptor 2 (Gene Name=Gria2); Q9Y698

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