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- PDB-6oe1: Benzensulfonamides bearing spyrohydantoin moieties act as potent ... -

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Basic information

Entry
Database: PDB / ID: 6oe1
TitleBenzensulfonamides bearing spyrohydantoin moieties act as potent inhibitors of human carbonic anhydrases II and VII and show neuropathic pain attenuating effects
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / carbonic anhydrase inhibitors / metalloenzymes / organoselenium / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
Chem-M8V / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPeat, T.S.
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Benzensulfonamides bearing spyrohydantoin moieties act as potent inhibitors of human carbonic anhydrases II and VII and show neuropathic pain attenuating effects.
Authors: Angeli, A. / Di Cesare Mannelli, L. / Ghelardini, C. / Peat, T.S. / Bartolucci, G. / Menicatti, M. / Carta, F. / Supuran, C.T.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9235
Polymers29,2891
Non-polymers6344
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-25 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.336, 41.447, 72.073
Angle α, β, γ (deg.)90.00, 104.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 320 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-M8V / 2-(2,4-dioxo-1,3-diazaspiro[4.5]decan-3-yl)-N-(4-sulfamoylphenyl)acetamide


Mass: 380.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N4O5S
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 200 nL 7 mg/mL protein + 200 nL reservoir (50 mM Tris, pH 8.0-8.2, 2.5-2.8 M ammonium sulfate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 13, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. obs: 39477 / % possible obs: 91.6 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.022 / Net I/σ(I): 21.5
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 8.3 / Num. unique obs: 1476 / CC1/2: 0.983 / Rpim(I) all: 0.063 / % possible all: 69.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C7X

6c7x


Resolution: 1.45→39.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.895 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.066 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.166 1997 5.1 %RANDOM
Rwork0.14734 ---
obs0.14835 37463 91.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.234 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0.08 Å2
2--0.03 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.45→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 38 316 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132318
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172084
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.6583172
X-RAY DIFFRACTIONr_angle_other_deg1.5331.6034893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22424.071113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51515390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.586157
X-RAY DIFFRACTIONr_chiral_restr0.1030.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022676
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02475
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_it1.0850.781120
X-RAY DIFFRACTIONr_mcbond_other1.0830.7781119
X-RAY DIFFRACTIONr_mcangle_it1.7011.1711428
X-RAY DIFFRACTIONr_mcangle_other1.71.1731429
X-RAY DIFFRACTIONr_scbond_it1.7870.9531198
X-RAY DIFFRACTIONr_scbond_other1.7790.9511193
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7151.3471739
X-RAY DIFFRACTIONr_long_range_B_refined4.06115.58310232
X-RAY DIFFRACTIONr_long_range_B_other4.06115.58310233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 86 -
Rwork0.156 2130 -
obs--69.62 %

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