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- PDB-2xx7: Crystal structure of 1-(4-(1-pyrrolidinylcarbonyl)phenyl)-3-(trif... -

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Basic information

Entry
Database: PDB / ID: 2xx7
TitleCrystal structure of 1-(4-(1-pyrrolidinylcarbonyl)phenyl)-3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazole in complex with the ligand binding domain of the Rat GluA2 receptor and glutamate at 2.2A resolution.
ComponentsGLUTAMATE RECEPTOR 2
KeywordsTRANSPORT PROTEIN / AMPA RECEPTOR LIGAND-BINDING CORE / ION CHANNEL
Function / homology
Function and homology information


spine synapse / dendritic spine cytoplasm / dendritic spine neck / cellular response to amine stimulus / dendritic spine head / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine cytoplasm / dendritic spine neck / cellular response to amine stimulus / dendritic spine head / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor clustering / kainate selective glutamate receptor activity / immunoglobulin binding / asymmetric synapse / AMPA glutamate receptor complex / regulation of receptor recycling / extracellularly glutamate-gated ion channel activity / cellular response to glycine / ionotropic glutamate receptor complex / conditioned place preference / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / response to fungicide / regulation of synaptic transmission, glutamatergic / cytoskeletal protein binding / glutamate-gated receptor activity / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / ionotropic glutamate receptor binding / dendrite membrane / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / synaptic membrane / dendritic shaft / SNARE binding / PDZ domain binding / synaptic transmission, glutamatergic / protein tetramerization / establishment of protein localization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / receptor internalization / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / long-term synaptic potentiation / synaptic vesicle membrane / amyloid-beta binding / presynapse / signaling receptor activity / growth cone / presynaptic membrane / scaffold protein binding / dendritic spine / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / external side of plasma membrane / axon / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / 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. / Periplasmic binding protein-like II / Receptor, 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. / Periplasmic binding protein-like II / Receptor, ligand binding region / Receptor family ligand binding region / D-Maltodextrin-Binding Protein; domain 2 / Periplasmic binding protein-like I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1ND / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsWard, S.E. / Harries, M. / Aldegheri, L. / Austin, N.E. / Ballantine, S. / Ballini, E. / Bradley, D.M. / Bax, B.D. / Clarke, B.P. / Harris, A.J. ...Ward, S.E. / Harries, M. / Aldegheri, L. / Austin, N.E. / Ballantine, S. / Ballini, E. / Bradley, D.M. / Bax, B.D. / Clarke, B.P. / Harris, A.J. / Harrison, S.A. / Melarange, R.A. / Mookherjee, C. / Mosley, J. / DalNegro, G. / Oliosi, B. / Smith, K.J. / Thewlis, K.M. / Woollard, P.M. / Yusaf, S.P.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Integration of Lead Optimization with Crystallography for a Membrane-Bound Ion Channel Target: Discovery of a New Class of Ampa Receptor Positive Allosteric Modulators.
Authors: Ward, S.E. / Harries, M. / Aldegheri, L. / Austin, N.E. / Ballantine, S. / Ballini, E. / Bradley, D.M. / Bax, B.D. / Clarke, B.P. / Harris, A.J. / Harrison, S.A. / Melarange, R.A. / ...Authors: Ward, S.E. / Harries, M. / Aldegheri, L. / Austin, N.E. / Ballantine, S. / Ballini, E. / Bradley, D.M. / Bax, B.D. / Clarke, B.P. / Harris, A.J. / Harrison, S.A. / Melarange, R.A. / Mookherjee, C. / Mosley, J. / Dal Negro, G. / Oliosi, B. / Smith, K.J. / Thewlis, K.M. / Woollard, P.M. / Yusaf, S.P.
History
DepositionNov 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Version format compliance
Revision 1.2Oct 23, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,14914
Polymers96,5583
Non-polymers1,59111
Water9,746541
1
A: GLUTAMATE RECEPTOR 2
C: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1607
Polymers64,3722
Non-polymers7885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-41 kcal/mol
Surface area22810 Å2
MethodPISA
2
B: GLUTAMATE RECEPTOR 2
hetero molecules

B: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,97714
Polymers64,3722
Non-polymers1,60612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2740 Å2
ΔGint-118.9 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.366, 161.901, 47.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 32185.889 Da / Num. of mol.: 3 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 413-527,653-795 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GLUA2 FLOP ISOFORM S1-DOMAIN-GLYTHR-S2-DOMAIN / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19491

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Non-polymers , 5 types, 552 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-1ND / 1-[4-(1-PYRROLIDINYLCARBONYL)PHENYL]-3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-INDAZOLE


Mass: 363.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20F3N3O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 775 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 775 TO SER ...ENGINEERED RESIDUE IN CHAIN A, ASN 775 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 775 TO SER ENGINEERED RESIDUE IN CHAIN C, ASN 775 TO SER
Has protein modificationY
Sequence detailsMUTATION N242S IS N775S IN UNIPROT NUMBERING.

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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: 2.2 Å3/Da / Density % sol: 43.54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 40273 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.8

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Processing

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

Resolution: 2.2→92.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.031 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21842 1629 4 %RANDOM
Rwork0.16588 ---
obs0.16802 38643 89.33 %-
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: 28.501 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→92.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 92 541 6679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226640
X-RAY DIFFRACTIONr_bond_other_d0.0010.024550
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9888999
X-RAY DIFFRACTIONr_angle_other_deg0.91311180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.065854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91724.567254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.766151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7221529
X-RAY DIFFRACTIONr_chiral_restr0.0890.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027444
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021290
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_it0.871.54118
X-RAY DIFFRACTIONr_mcbond_other0.1811.51701
X-RAY DIFFRACTIONr_mcangle_it1.61726650
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.41432522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8814.52349
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: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 114 -
Rwork0.2 2900 -
obs--92 %

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