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Yorodumi- PDB-6ex1: Crystal structure of human carbonic anhydrase I in complex with t... -
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-Basic information
Entry | Database: PDB / ID: 6ex1 | ||||||
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Title | Crystal structure of human carbonic anhydrase I in complex with the 4-[(3S)-3 benzyl-4-(4-sulfamoylbenzoyl)piperazine -1-carbonyl]benzene-1-sulfonamide inhibitor | ||||||
Components | Carbonic anhydrase 1 | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Ferraroni, M. / Supuran, C.T. / Chiapponi, D. / Chiaramonte, N. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2018 Title: 2-Benzylpiperazine: A new scaffold for potent human carbonic anhydrase inhibitors. Synthesis, enzyme inhibition, enantioselectivity, computational and crystallographic studies and in vivo ...Title: 2-Benzylpiperazine: A new scaffold for potent human carbonic anhydrase inhibitors. Synthesis, enzyme inhibition, enantioselectivity, computational and crystallographic studies and in vivo activity for a new class of intraocular pressure lowering agents. Authors: Chiaramonte, N. / Bua, S. / Ferraroni, M. / Nocentini, A. / Bonardi, A. / Bartolucci, G. / Durante, M. / Lucarini, L. / Chiapponi, D. / Dei, S. / Manetti, D. / Teodori, E. / Gratteri, P. / ...Authors: Chiaramonte, N. / Bua, S. / Ferraroni, M. / Nocentini, A. / Bonardi, A. / Bartolucci, G. / Durante, M. / Lucarini, L. / Chiapponi, D. / Dei, S. / Manetti, D. / Teodori, E. / Gratteri, P. / Masini, E. / Supuran, C.T. / Romanelli, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ex1.cif.gz | 122.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ex1.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ex1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/6ex1 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/6ex1 | HTTPS FTP |
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-Related structure data
Related structure data | 6evrC 1jv0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28906.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00915, carbonic anhydrase |
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-Non-polymers , 5 types, 327 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.12 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 28% PEG4000, 0.2 M Sodium acetate, Tris 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 15, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→30 Å / Num. obs: 72418 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.166 % / Biso Wilson estimate: 39.256 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.086 / Χ2: 0.999 / Net I/σ(I): 7.27 / Num. measured all: 229251 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1JV0 Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.839 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.328 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→30 Å
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Refine LS restraints |
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