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- PDB-2xhd: Crystal structure of N-((2S)-5-(6-fluoro-3-pyridinyl)-2,3-dihydro... -

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Basic information

Entry
Database: PDB / ID: 2xhd
TitleCrystal 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
ComponentsGLUTAMATE RECEPTOR 2
KeywordsTRANSPORT PROTEIN / ION CHANNEL
Function / homology
Function and homology information


Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / asymmetric synapse / excitatory synapse ...Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / asymmetric synapse / excitatory synapse / glutamate-gated receptor activity / MECP2 regulates neuronal receptors and channels / ionotropic glutamate receptor signaling pathway / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / endocytic vesicle membrane / amyloid-beta binding / chemical synaptic transmission / postsynapse / dendritic spine / postsynaptic density / external side of plasma membrane / neuronal cell body / dendrite / signal transduction / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7T9 / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.8 Å
AuthorsWard, S.E. / Harries, M. / Aldegheri, L. / Andreotti, D. / Ballantine, S. / Bax, B.D. / Harris, A.J. / Harker, A.J. / Lund, J. / Melarange, R. ...Ward, S.E. / Harries, M. / Aldegheri, L. / Andreotti, D. / Ballantine, S. / Bax, B.D. / Harris, A.J. / Harker, A.J. / Lund, J. / Melarange, R. / Mingardi, A. / Mookherjee, C. / Mosley, J. / Neve, M. / Oliosi, B. / Profeta, R. / Smith, K.J. / Smith, P.W. / Spada, S. / Thewlis, K.M. / Yusaf, S.P.
CitationJournal: J.Med.Chem. / Year: 2010
Title: 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.
Authors: Ward, S.E. / Harries, M. / Aldegheri, L. / Andreotti, D. / Ballantine, S. / Bax, B.D. / Harris, A.J. / Harker, A.J. / Lund, J. / Melarange, R. / Mingardi, A. / Mookherjee, C. / Mosley, J. / ...Authors: Ward, S.E. / Harries, M. / Aldegheri, L. / Andreotti, D. / Ballantine, S. / Bax, B.D. / Harris, A.J. / Harker, A.J. / Lund, J. / Melarange, R. / Mingardi, A. / Mookherjee, C. / Mosley, J. / Neve, M. / Oliosi, B. / Profeta, R. / Smith, K.J. / Smith, P.W. / Spada, S. / Thewlis, K.M. / Yusaf, S.P.
History
DepositionJun 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,66510
Polymers58,5562
Non-polymers1,1098
Water9,818545
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-72.8 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.139, 121.781, 47.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GLUTAMATE RECEPTOR 2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC AMPA 2 / GLUA2 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 2


Mass: 29277.814 Da / Num. of mol.: 2
Fragment: LIGAND BINDING DOMAIN, RESIDUES 412-427 AND 653-796
Source method: isolated from a genetically manipulated source
Details: THIS IS AN S1-S2 FUSION IN WHICH GLY 118 AND THR 119 REPLACE A MEMBRANE SPANNING REGION.
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42262
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-7T9 / N-[(2S)-5-(6-FLUORO-3-PYRIDINYL)-2,3-DIHYDRO-1H-INDEN-2-YL]-2-PROPANESULFONAMIDE


Mass: 334.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19FN2O2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsN-[(2S)-5-(6-FLUORO-3-PYRIDINYL)-2, 3-DIHYDRO-1H-INDEN-2-YL]-2-PROPANESULFONAMIDE (7T9): COMPOUND ...N-[(2S)-5-(6-FLUORO-3-PYRIDINYL)-2, 3-DIHYDRO-1H-INDEN-2-YL]-2-PROPANESULFONAMIDE (7T9): COMPOUND SITS ON NON-CRYSTALLOGRAPHIC TWOFOLD. TWO EQUIVALENT BINDING MODES ARE OBSEREVED. GLUTAMATE (GLU): GLUTAMATE IS THE LIGAND FOR THE RECEPTOR.
Sequence detailsTHIS IS AN S1-S2 FUSION IN WHICH GLY 118 AND THR 119 REPLACE A MEMBRANE SPANNING REGION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.75 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 53509 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKLdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.992 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COMPOUND 7T9 ON POCKET ON NCS TWOFOLD AXIS THE OCCUPANCY FOR THE COMPOUND AND SOME ASSOCIATED WATERS AND SIDE-CHAINS ARE 0.5. WATERS 3000- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COMPOUND 7T9 ON POCKET ON NCS TWOFOLD AXIS THE OCCUPANCY FOR THE COMPOUND AND SOME ASSOCIATED WATERS AND SIDE-CHAINS ARE 0.5. WATERS 3000-3003 ARE ASSOCIATED ASSOCIATED WITH CONFORMER B, 3004-3007 WITH CONFORMER A
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2702 5.1 %RANDOM
Rwork0.2 ---
obs0.202 50730 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å20 Å2
2---1.2 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 68 545 4631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224383
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.9935943
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7455556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.59424.269171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16515819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4431523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213309
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7122688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50454357
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.27261695
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6381586
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 194 -
Rwork0.246 3574 -
obs--100 %

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