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- PDB-6pgx: Synthesis of novel tellurides bearing benzensulfonamide moiety as... -

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Basic information

Entry
Database: PDB / ID: 6pgx
TitleSynthesis of novel tellurides bearing benzensulfonamide moiety as carbonic anhydrase inhibitors with antitumor activity
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Carbonic Anhydrase Inhibitors (CAIs) / tellurium / metalloenzymes / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / 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-OJ4 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsPeat, T.S.
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Synthesis of novel tellurides bearing benzensulfonamide moiety as carbonic anhydrase inhibitors with antitumor activity.
Authors: Tanini, D. / Ricci, L. / Capperucci, A. / Di Cesare Mannelli, L. / Ghelardini, C. / Peat, T.S. / Carta, F. / Angeli, A. / Supuran, C.T.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3037
Polymers29,2891
Non-polymers2,0146
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-7 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.458, 41.380, 72.430
Angle α, β, γ (deg.)90.00, 104.41, 90.00
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-OJ4 / 4-[(2S)-2-hydroxy-3-{[(2R)-2-hydroxy-3-(4-sulfamoylphenoxy)propyl]tellanyl}propoxy]benzene-1-sulfonamide


Mass: 588.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H24N2O8S2Te / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 250 nL 7.5 mg/mL protein + 225 nL well solution (2.5-3.0 M ammonium sulfate, 100 mM Tris buffer, pH 8.0-8.5) + 25 nL microseeds
PH range: 8.0-8.5

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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: Feb 14, 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: 1.36→41.4 Å / Num. obs: 51332 / % possible obs: 97.6 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.028 / Net I/σ(I): 15.3
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2429 / CC1/2: 0.893 / Rpim(I) all: 0.199 / % possible all: 92.4

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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 6ODZ

6odz


Resolution: 1.36→40.13 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.489 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.048 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15237 2537 4.9 %RANDOM
Rwork0.11781 ---
obs0.11944 48780 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å2-0.14 Å2
2--0.07 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.36→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 76 268 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132313
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172078
X-RAY DIFFRACTIONr_angle_refined_deg1.851.6773154
X-RAY DIFFRACTIONr_angle_other_deg1.5351.6164867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59823.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76415379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.532157
X-RAY DIFFRACTIONr_chiral_restr0.0930.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02491
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_it1.1741.1451099
X-RAY DIFFRACTIONr_mcbond_other1.171.1421098
X-RAY DIFFRACTIONr_mcangle_it1.6021.7291393
X-RAY DIFFRACTIONr_mcangle_other1.6061.7321394
X-RAY DIFFRACTIONr_scbond_it2.0661.4631214
X-RAY DIFFRACTIONr_scbond_other2.0661.4631215
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4672.0711762
X-RAY DIFFRACTIONr_long_range_B_refined3.23623.4489918
X-RAY DIFFRACTIONr_long_range_B_other3.23623.4499919
X-RAY DIFFRACTIONr_rigid_bond_restr1.77134391
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.359→1.394 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 171 -
Rwork0.183 3440 -
obs--92.95 %

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