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- PDB-7bfa: 4-(2-(3-(4-iodophenyl)thioureido)ethyl)benzenesulfonamide in comp... -

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Basic information

Entry
Database: PDB / ID: 7bfa
Title4-(2-(3-(4-iodophenyl)thioureido)ethyl)benzenesulfonamide in complex with Carbonic Anhydrase II
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase II / inhibitors / sulfonamide
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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / 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 / cytoplasm / cytosol
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-TKE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAngeli, A. / Ferraroni, M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structural Insights into Schistosoma mansoni Carbonic Anhydrase (SmCA) Inhibition by Selenoureido-Substituted Benzenesulfonamides.
Authors: Angeli, A. / Ferraroni, M. / Da'dara, A.A. / Selleri, S. / Pinteala, M. / Carta, F. / Skelly, P.J. / Supuran, C.T.
History
DepositionJan 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9084
Polymers29,2891
Non-polymers6193
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-6 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.450, 41.600, 72.250
Angle α, β, γ (deg.)90.000, 104.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TKE / 1-(4-iodophenyl)-3-[2-(4-sulfamoylphenyl)ethyl]thiourea


Mass: 461.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16IN3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5-1.7 M sodium citrate 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.6→41.6 Å / Num. obs: 31428 / % possible obs: 97.1 % / Redundancy: 12.3 % / CC1/2: 0.89 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Rrim(I) all: 0.066 / Net I/σ(I): 28.5
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.122 / Num. unique obs: 1482 / CC1/2: 0.65 / Rpim(I) all: 0.052 / Rrim(I) all: 0.133

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIK

4fik


Resolution: 1.6→40.121 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.307 / SU ML: 0.047 / Cross valid method: NONE / ESU R: 0.081 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.182 1531 4.878 %
Rwork0.1461 29856 -
all0.148 --
obs-31387 96.62 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.108 Å2-0 Å20.056 Å2
2---0.235 Å20 Å2
3---0.086 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 30 205 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132199
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172024
X-RAY DIFFRACTIONr_angle_refined_deg1.871.6373004
X-RAY DIFFRACTIONr_angle_other_deg1.4641.5974701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0545280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22823.796108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4615361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.541157
X-RAY DIFFRACTIONr_chiral_restr0.090.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
X-RAY DIFFRACTIONr_nbd_refined0.2450.2407
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21920
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21025
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21003
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.210
X-RAY DIFFRACTIONr_nbd_other0.1720.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.220
X-RAY DIFFRACTIONr_mcbond_it1.4661.0761055
X-RAY DIFFRACTIONr_mcbond_other1.4671.0791056
X-RAY DIFFRACTIONr_mcangle_it2.2631.6061320
X-RAY DIFFRACTIONr_mcangle_other2.2831.6091321
X-RAY DIFFRACTIONr_scbond_it3.0131.3171144
X-RAY DIFFRACTIONr_scbond_other3.0111.3171145
X-RAY DIFFRACTIONr_scangle_it4.5841.8791672
X-RAY DIFFRACTIONr_scangle_other4.5831.881673
X-RAY DIFFRACTIONr_lrange_it4.99313.1212429
X-RAY DIFFRACTIONr_lrange_other4.99213.1272430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.21970.1322147X-RAY DIFFRACTION94.2066
1.642-1.6870.2930.1482127X-RAY DIFFRACTION95.6484
1.687-1.7350.2741090.1842043X-RAY DIFFRACTION95.4324
1.735-1.7890.2041040.1731976X-RAY DIFFRACTION95.2381
1.789-1.8470.1771000.1441968X-RAY DIFFRACTION95.5196
1.847-1.9120.1841010.1441874X-RAY DIFFRACTION96.9087
1.912-1.9840.2011200.1411818X-RAY DIFFRACTION96.6102
1.984-2.0650.192980.1461750X-RAY DIFFRACTION96.7539
2.065-2.1570.183910.1441672X-RAY DIFFRACTION96.7618
2.157-2.2620.168780.1411650X-RAY DIFFRACTION97.0787
2.262-2.3840.163780.1451545X-RAY DIFFRACTION97.1275
2.384-2.5290.208790.1461468X-RAY DIFFRACTION97.4181
2.529-2.7030.167860.141378X-RAY DIFFRACTION97.6651
2.703-2.9190.152680.1521289X-RAY DIFFRACTION97.6962
2.919-3.1980.199540.1571221X-RAY DIFFRACTION98.0769
3.198-3.5740.164560.151081X-RAY DIFFRACTION98.0172
3.574-4.1250.152380.119983X-RAY DIFFRACTION98.6473
4.125-5.0480.104200.104845X-RAY DIFFRACTION98.4073
5.048-7.120.215420.167647X-RAY DIFFRACTION98.5694
7.12-40.1210.169190.169374X-RAY DIFFRACTION97.7612

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