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- PDB-5wex: Discovery of new selenoureido analogs of 4-(4-fluorophenylureido)... -

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Basic information

Entry
Database: PDB / ID: 5wex
TitleDiscovery of new selenoureido analogs of 4-(4-fluorophenylureido) benzenesulfonamides as carbonic anhydrase inhibitors
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Carbonic Anhydrase Inhibitors / Metalloenzymes / Glutathione Peroxidase / 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 / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-8JS / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.26 Å
AuthorsAngeli, A. / Tanini, D. / Peat, T.S. / Di Cesare Mannelli, L. / Bartolucci, G. / Capperucci, A. / Ghelardini, C. / Supuran, C.T. / Carta, F.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Discovery of New Selenoureido Analogues of 4-(4-Fluorophenylureido)benzenesulfonamide as Carbonic Anhydrase Inhibitors.
Authors: Angeli, A. / Tanini, D. / Peat, T.S. / Di Cesare Mannelli, L. / Bartolucci, G. / Capperucci, A. / Ghelardini, C. / Supuran, C.T. / Carta, F.
History
DepositionJul 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)29,8505
Polymers29,2891
Non-polymers5614
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-5 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.472, 41.502, 72.350
Angle α, β, γ (deg.)90.00, 104.39, 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, 241 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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-8JS / 4-{[(4-fluorophenyl)carbamothioyl]amino}benzene-1-sulfonamide


Mass: 325.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12FN3O2S2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: concentrated CA II at about 10 mg/mL was set up in SD-2 plates with the following ratio of protein plus reservoir plus seeds: 250nL plus 225 nL plus 25 nL. The plate was incubated at 8C and ...Details: concentrated CA II at about 10 mg/mL was set up in SD-2 plates with the following ratio of protein plus reservoir plus seeds: 250nL plus 225 nL plus 25 nL. The plate was incubated at 8C and the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8. 3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.26→41.1 Å / Num. obs: 63929 / % possible obs: 96.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rsym value: 0.089 / Net I/σ(I): 10.6
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 6 % / Rmerge(I) obs: 1.175 / Mean I/σ(I) obs: 2 / Num. unique obs: 3012 / CC1/2: 0.609 / Rpim(I) all: 0.511 / Rsym value: 1.286 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.26→41.1 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.297 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14655 3108 4.9 %RANDOM
Rwork0.11785 ---
obs0.1193 60631 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.971 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20.02 Å2
2---0.34 Å20 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.26→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 32 237 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192304
X-RAY DIFFRACTIONr_bond_other_d0.0020.022093
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9643149
X-RAY DIFFRACTIONr_angle_other_deg1.0334911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49925.049103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60815393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.224157
X-RAY DIFFRACTIONr_chiral_restr0.1310.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212654
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02473
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_it1.7951.4061118
X-RAY DIFFRACTIONr_mcbond_other1.7921.4021117
X-RAY DIFFRACTIONr_mcangle_it2.3642.1231424
X-RAY DIFFRACTIONr_mcangle_other2.3752.1261425
X-RAY DIFFRACTIONr_scbond_it2.9891.7421186
X-RAY DIFFRACTIONr_scbond_other2.9961.7431187
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4142.4751722
X-RAY DIFFRACTIONr_long_range_B_refined3.59728.3089889
X-RAY DIFFRACTIONr_long_range_B_other3.59728.3099890
X-RAY DIFFRACTIONr_rigid_bond_restr2.78834397
X-RAY DIFFRACTIONr_sphericity_free24.468565
X-RAY DIFFRACTIONr_sphericity_bonded10.98154492
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 225 -
Rwork0.187 4271 -
obs--92.49 %

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