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(-) Description

Title :  CRYSTAL STRUCTURE OF N-((2S)-5-(6-FLUORO-3-PYRIDINYL)-2,3-DIHYDRO-1H-INDEN-2-YL)-2-PROPANESULFONAMIDE IN COMPLEX WITH THE LIGAND BINDING DOMAIN OF THE HUMAN GLUA2 RECEPTOR
 
Authors :  S. E. Ward, M. Harries, L. Aldegheri, D. Andreotti, S. Ballantine, B. D. A. J. Harris, A. J. Harker, J. Lund, R. Melarange, A. Mingardi, C. Mookh J. Mosley, M. Neve, B. Oliosi, R. Profeta, K. J. Smith, P. W. Smith, S. Sp K. M. Thewlis, S. P. Yusaf
Date :  14 Jun 10  (Deposition) - 21 Jul 10  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport Protein, Ion Channel (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. E. Ward, M. Harries, L. Aldegheri, D. Andreotti, S. Ballantine, B. D. Bax, A. J. Harris, A. J. Harker, J. Lund, R. Melarange, A. Mingardi C. Mookherjee, J. Mosley, M. Neve, B. Oliosi, R. Profeta, K. J. Smith, P. W. Smith, S. Spada, K. M. Thewlis, S. P. Yusaf
Discovery Of N-[(2S)-5-(6-Fluoro-3-Pyridinyl)-2, 3- Dihydro-1H-Inden-2-Yl]-2-Propanesulfonamide, A Novel Clinical Ampa Receptor Positive Modulator.
J. Med. Chem. V. 53 5801 2010
PubMed-ID: 20614889  |  Reference-DOI: 10.1021/JM1005429

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentLIGAND BINDING DOMAIN, RESIDUES 412-427 AND 653-796
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHIS IS AN S1-S2 FUSION IN WHICH GLY 118 AND THR 119 REPLACE A MEMBRANE SPANNING REGION.
    SynonymGLUR-B, GLUR-K2, GLUTAMATE RECEPTOR IONOTROPIC AMPA 2, GLUA2, AMPA-SELECTIVE GLUTAMATE RECEPTOR 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
17T91Ligand/IonN-[(2S)-5-(6-FLUORO-3-PYRIDINYL)-2,3-DIHYDRO-1H-INDEN-2-YL]-2-PROPANESULFONAMIDE
2GLU2Mod. Amino AcidGLUTAMIC ACID
3SO45Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:61 , PRO A:89 , LEU A:90 , THR A:91 , ARG A:96 , GLY A:141 , SER A:142 , THR A:143 , GLU A:193 , TYR A:220 , HOH A:2148 , HOH A:2205 , HOH A:2283BINDING SITE FOR RESIDUE GLU A 301
2AC2SOFTWARESER A:140 , LYS A:144 , ARG A:148 , HOH A:2150 , HOH A:2284 , HOH A:2285 , HOH A:2286BINDING SITE FOR RESIDUE SO4 A1264
3AC3SOFTWAREARG A:148 , TRP A:159 , ARG A:163BINDING SITE FOR RESIDUE SO4 A1265
4AC4SOFTWARETYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , GLY B:141 , SER B:142 , THR B:143 , GLU B:193 , TYR B:220 , HOH B:2138 , HOH B:2185 , HOH B:2245BINDING SITE FOR RESIDUE GLU B 301
5AC5SOFTWAREASP B:139 , SER B:140 , LYS B:144 , ARG B:148 , HOH B:2081 , HOH B:2246 , HOH B:2247 , HOH B:2248BINDING SITE FOR RESIDUE SO4 B1263
6AC6SOFTWARELYS A:183 , ARG B:31 , HOH B:2040 , HOH B:2249 , HOH B:2250BINDING SITE FOR RESIDUE SO4 B1264
7AC7SOFTWAREARG B:148 , TRP B:159 , ARG B:163 , HOH B:2251BINDING SITE FOR RESIDUE SO4 B1265
8AC8SOFTWARELYS A:104 , PRO A:105 , MET A:107 , SER A:108 , SER A:217 , LYS A:218 , GLY A:219 , SER A:242 , HOH A:2234 , HOH A:2257 , LYS B:104 , PRO B:105 , MET B:107 , SER B:108 , SER B:217 , LYS B:218 , GLY B:219 , SER B:242 , HOH B:3000 , HOH B:3001 , HOH B:3002 , HOH B:3003 , HOH B:3004 , HOH B:3005 , HOH B:3006 , HOH B:3007BINDING SITE FOR RESIDUE 7T9 B1266

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:206 -A:261
2B:206 -B:261

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:14 -Pro A:15
2Glu A:166 -Pro A:167
3Lys A:204 -Pro A:205
4Ser B:14 -Pro B:15
5Glu B:166 -Pro B:167
6Lys B:204 -Pro B:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XHD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XHD)

(-) Exons   (0, 0)

(no "Exon" information available for 2XHD)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:262
 aligned with GRIA2_HUMAN | P42262 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:391
                                   422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802 
          GRIA2_HUMAN   413 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGSGGGDSKE 803
               SCOP domains d2xhda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -2xhdA01 A:4-109,A:219-258 Periplasmic binding protein-like II                                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2xhdA01 A:4-109,A:219-258               ------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh........------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhd A   3 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYDKGECGA------E 301
                                    12        22        32        42        52        62        72        82        92       102       112     |   -         -         -         -         -         -         -         -         -         -         -         -       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259   |     -|
                                                                                                                                             118                                                                                                                         119                                                                                                                                             263    301

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with GRIA2_HUMAN | P42262 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:390
                                   423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803
          GRIA2_HUMAN   414 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGSGGGDSKE 803
               SCOP domains d2xhdb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2xhdB01 B:4-109,B:219-262 Periplasmic binding protein-like II                                             ---------                                                                                                                           ----------------------------------------------------------------------------------------------------2xhdB01 B:4-109,B:219-262                          - CATH domains
           Pfam domains (1) -----------Lig_chan-Glu_bd-2xhdB03 B:15-80                                   --------------------------------------                                                                                                                           -Lig_chan-2xhdB01 B:120-262                                                                                                                            - Pfam domains (1)
           Pfam domains (2) -----------Lig_chan-Glu_bd-2xhdB04 B:15-80                                   --------------------------------------                                                                                                                           -Lig_chan-2xhdB02 B:120-262                                                                                                                            - Pfam domains (2)
         Sec.struct. author ..eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.---..-------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xhd B   4 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRTPVNLAVLKLSEQGVLDKLKNKWWYD---CG-------E 301
                                    13        23        33        43        53        63        73        83        93       103       113    |    -         -         -         -         -         -         -         -         -         -         -         -       120       130       140       150       160       170       180       190       200       210       220       230       240       250      |  -||     301
                                                                                                                                            118                                                                                                                         119                                                                                                                                       257 261|     301
                                                                                                                                                                                                                                                                                                                                                                                                                       262        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRIA2_HUMAN | P42262)
molecular function
    GO:0004971    AMPA glutamate receptor activity    An ionotropic glutamate receptor activity that exhibits fast gating by glutamate and acts by opening a cation channel permeable to sodium, potassium, and, in the absence of a GluR2 subunit, calcium.
    GO:0005231    excitatory extracellular ligand-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts, where channel opening contributes to an increase in membrane potential.
    GO:0005234    extracellular-glutamate-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when extracellular glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0004970    ionotropic glutamate receptor activity    Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0035235    ionotropic glutamate receptor signaling pathway    A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0032281    AMPA glutamate receptor complex    An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0030666    endocytic vesicle membrane    The lipid bilayer surrounding an endocytic vesicle.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GRIA2_HUMAN | P422622wjw 2wjx 3r7x 3rn8 3rnn 3ua8 5h8s

(-) Related Entries Specified in the PDB File

2wjw CRYSTAL STRUCTURE OF THE HUMAN IONOTROPIC GLUTAMATE RECEPTOR GLUR2 ATD REGION AT 1.8 A RESOLUTION
2wjx CRYSTAL STRUCTURE OF THE HUMAN IONOTROPIC GLUTAMATE RECEPTOR GLUR2 ATD REGION AT 4.1 A RESOLUTION