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- PDB-5cgd: Structure of the human class C GPCR metabotropic glutamate recept... -
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Basic information
Entry | Database: PDB / ID: 5cgd | ||||||
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Title | Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile - (HTL14242) | ||||||
![]() | Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5 | ||||||
![]() | SIGNALING PROTEIN / 7TM / Receptor / GPCR / Membrane-Protein | ||||||
Function / homology | ![]() A2A adenosine receptor binding / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / protein tyrosine kinase activator activity / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway ...A2A adenosine receptor binding / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / protein tyrosine kinase activator activity / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / Class C/3 (Metabotropic glutamate/pheromone receptors) / : / glutamate receptor activity / Neurexins and neuroligins / viral release from host cell by cytolysis / regulation of synaptic transmission, glutamatergic / positive regulation of calcium-mediated signaling / peptidoglycan catabolic process / protein tyrosine kinase binding / learning / dendritic shaft / locomotory behavior / G protein-coupled receptor activity / synapse organization / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cognition / cellular response to amyloid-beta / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (q) signalling events / chemical synaptic transmission / host cell cytoplasm / positive regulation of MAPK cascade / learning or memory / dendritic spine / defense response to bacterium / glutamatergic synapse / dendrite / regulation of DNA-templated transcription / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Christopher, J.A. / Aves, S.J. / Bennett, K.A. / Dore, A.S. / Errey, J.C. / Jazayeri, A. / Marshall, F.H. / Okrasa, K. / Serrano-Vega, M.J. / Tehan, B.G. ...Christopher, J.A. / Aves, S.J. / Bennett, K.A. / Dore, A.S. / Errey, J.C. / Jazayeri, A. / Marshall, F.H. / Okrasa, K. / Serrano-Vega, M.J. / Tehan, B.G. / Wiggin, G.R. / Congreve, M. | ||||||
![]() | ![]() Title: Fragment and Structure-Based Drug Discovery for a Class C GPCR: Discovery of the mGlu5 Negative Allosteric Modulator HTL14242 (3-Chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile). Authors: Christopher, J.A. / Aves, S.J. / Bennett, K.A. / Dore, A.S. / Errey, J.C. / Jazayeri, A. / Marshall, F.H. / Okrasa, K. / Serrano-Vega, M.J. / Tehan, B.G. / Wiggin, G.R. / Congreve, M. #1: ![]() Title: Structure of class C GPCR metabotropic glutamate receptor 5 transmembrane domain. Authors: Dore, A.S. / Okrasa, K. / Patel, J.C. / Serrano-Vega, M. / Bennett, K. / Cooke, R.M. / Errey, J.C. / Jazayeri, A. / Khan, S. / Tehan, B. / Weir, M. / Wiggin, G.R. / Marshall, F.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 98.8 KB | Display | ![]() |
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PDB format | ![]() | 72.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5cgcC ![]() 4oo9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49802.531 Da / Num. of mol.: 1 Mutation: E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A,E579A N667Y I669A G675M C1054T C1097A T742A S753A Source method: isolated from a genetically manipulated source Details: mGluR5 transmembrane domain from Homo Sapiens fused with T4-Lysozyme from Enterobacteria Phage T4 in complex with the new chemical entity (NCE): 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile Source: (gene. exp.) ![]() ![]() Gene: GRM5, GPRC1E, MGLUR5 / Cell line (production host): Sf21 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-OLA / #3: Chemical | ChemComp-51E / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 293.1 K / Method: lipidic cubic phase / pH: 6.8 Details: 24-34% V/V PEG400, 0.2 M AMMONIUM PHOSPHATE DIBASIC, 0.1 M MES, PH 6.8, |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→34.51 Å / Num. obs: 14891 / % possible obs: 95.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.43 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OO9 Resolution: 2.603→29.747 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.603→29.747 Å
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Refine LS restraints |
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LS refinement shell |
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