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Yorodumi- PDB-7qhd: Human Butyrylcholinesterase in complex with (S)-1-(4-((2-(1H-indo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qhd | ||||||
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Title | Human Butyrylcholinesterase in complex with (S)-1-(4-((2-(1H-indol-3-yl)ethyl)carbamoyl)benzyl)-N-(3-((1,2,3,4-tetrahydroacridin-9-yl)amino)propyl)piperidine-3-carboxamide | ||||||
Components | Cholinesterase | ||||||
Keywords | HYDROLASE / Butyrylcholinesterase / Inhibitor / Complex | ||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / acetylcholinesterase activity / choline metabolic process / hydrolase activity, acting on ester bonds / Aspirin ADME / nuclear envelope lumen / Synthesis of PC / Synthesis, secretion, and deacylation of Ghrelin / catalytic activity / response to glucocorticoid / xenobiotic metabolic process / learning / amyloid-beta binding / blood microparticle / negative regulation of cell population proliferation / endoplasmic reticulum lumen / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Brazzolotto, X. / Jing, L. / Zhan, P. / Liu, X. / Nachon, F. | ||||||
Funding support | France, 1items
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Citation | Journal: Bioorg.Chem. / Year: 2023 Title: Rapid discovery and crystallography study of highly potent and selective butylcholinesterase inhibitors based on oxime-containing libraries and conformational restriction strategies. Authors: Jing, L. / Wei, W. / Meng, B. / Chantegreil, F. / Nachon, F. / Martinez, A. / Wu, G. / Zhao, H. / Song, Y. / Kang, D. / Brazzolotto, X. / Zhan, P. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qhd.cif.gz | 292.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qhd.ent.gz | 195.8 KB | Display | PDB format |
PDBx/mmJSON format | 7qhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/7qhd ftp://data.pdbj.org/pub/pdb/validation_reports/qh/7qhd | HTTPS FTP |
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-Related structure data
Related structure data | 7qheC 1p0iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59713.512 Da / Num. of mol.: 1 Mutation: N17Q, N455Q, N481Q, N486Q mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase |
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-Sugars , 4 types, 7 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #8: Sugar | ChemComp-SIA / | |
-Non-polymers , 6 types, 311 molecules
#5: Chemical | ChemComp-MES / | ||||||||
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#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-C0I / ( | #9: Chemical | ChemComp-SO4 / #10: Chemical | ChemComp-CL / #11: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979184 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→77.26 Å / Num. obs: 48566 / % possible obs: 98.16 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.86 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06498 / Rpim(I) all: 0.02574 / Rrim(I) all: 0.07013 / Net I/σ(I): 16.23 |
Reflection shell | Resolution: 2.04→2.113 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.7103 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4792 / CC1/2: 0.796 / CC star: 0.941 / Rpim(I) all: 0.2867 / Rrim(I) all: 0.7684 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1p0i Resolution: 2.04→77.26 Å / SU ML: 0.2256 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6766 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 45.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→77.26 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.9808877912 Å / Origin y: 32.1835069911 Å / Origin z: 38.5677705179 Å
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Refinement TLS group | Selection details: chain 'A' |