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- PDB-7bg5: 4-(2-(3-(4-iodophenyl)ureido)ethyl)benzenesulfonamide in complex ... -

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Basic information

Entry
Database: PDB / ID: 7bg5
Title4-(2-(3-(4-iodophenyl)ureido)ethyl)benzenesulfonamide in complex with Carbonic Anhydrase II
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase II / inhibitor / 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-TKQ / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.428 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 5, 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)29,8924
Polymers29,2891
Non-polymers6033
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-7 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.362, 41.521, 71.969
Angle α, β, γ (deg.)90.000, 104.359, 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-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-TKQ / 1-(4-iodophenyl)-3-[2-(4-sulfamoylphenyl)ethyl]urea


Mass: 445.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16IN3O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.5 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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.428→35.7 Å / Num. obs: 87572 / % possible obs: 99.2 % / Redundancy: 3.23 % / CC1/2: 0.99 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.042 / Rsym value: 0.038 / Net I/σ(I): 20.14
Reflection shellResolution: 1.428→1.51 Å / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 8.18 / Num. unique obs: 14196 / CC1/2: 0.985 / Rrim(I) all: 0.122 / Rsym value: 0.136

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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: 1.428→35.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.768 / SU ML: 0.031 / Cross valid method: NONE / ESU R: 0.056 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1649 2323 5.149 %
Rwork0.1443 42795 -
all0.145 --
obs-45118 99.728 %
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: 13.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.154 Å2-0 Å2-0.029 Å2
2--0.001 Å2-0 Å2
3---0.149 Å2
Refinement stepCycle: LAST / Resolution: 1.428→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 30 236 2313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132188
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172011
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.6342983
X-RAY DIFFRACTIONr_angle_other_deg1.4811.5964664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16823.611108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8915355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.152157
X-RAY DIFFRACTIONr_chiral_restr0.1030.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
X-RAY DIFFRACTIONr_nbd_refined0.2540.2422
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.21952
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21028
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2151
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.211
X-RAY DIFFRACTIONr_nbd_other0.2260.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.220
X-RAY DIFFRACTIONr_mcbond_it1.6571.231048
X-RAY DIFFRACTIONr_mcbond_other1.6571.2321049
X-RAY DIFFRACTIONr_mcangle_it2.4311.8441309
X-RAY DIFFRACTIONr_mcangle_other2.3371.8451309
X-RAY DIFFRACTIONr_scbond_it4.7691.5141140
X-RAY DIFFRACTIONr_scbond_other4.7671.5191141
X-RAY DIFFRACTIONr_scangle_it6.762.1611666
X-RAY DIFFRACTIONr_scangle_other6.7752.1681667
X-RAY DIFFRACTIONr_lrange_it5.57415.5792461
X-RAY DIFFRACTIONr_lrange_other5.49615.5442459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.428-1.4650.181660.1473145X-RAY DIFFRACTION99.3996
1.465-1.5050.1741510.1453073X-RAY DIFFRACTION100
1.505-1.5490.1851650.1382990X-RAY DIFFRACTION100
1.549-1.5970.1541900.1332869X-RAY DIFFRACTION99.9673
1.597-1.6490.191410.142815X-RAY DIFFRACTION100
1.649-1.7070.191450.1412725X-RAY DIFFRACTION100
1.707-1.7710.1891310.142657X-RAY DIFFRACTION100
1.771-1.8430.1591260.1462542X-RAY DIFFRACTION99.6266
1.843-1.9250.1741280.1472435X-RAY DIFFRACTION99.961
1.925-2.0190.1971330.1412308X-RAY DIFFRACTION99.9181
2.019-2.1280.169900.1392226X-RAY DIFFRACTION99.8276
2.128-2.2570.1381240.1372078X-RAY DIFFRACTION99.5029
2.257-2.4130.1481100.1361957X-RAY DIFFRACTION99.8069
2.413-2.6060.1911080.1531838X-RAY DIFFRACTION99.6416
2.606-2.8540.182860.1561705X-RAY DIFFRACTION99.6661
2.854-3.1910.181880.1541530X-RAY DIFFRACTION99.5692
3.191-3.6830.161690.1481364X-RAY DIFFRACTION99.7911
3.683-4.5080.128700.1221146X-RAY DIFFRACTION99.1035
4.508-6.3610.141690.141875X-RAY DIFFRACTION98.8482
6.361-35.70.162330.162517X-RAY DIFFRACTION98.2143

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