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- PDB-5umc: Synthesis of novel seleno ureido containing compounds as SLC-0111... -

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Basic information

Entry
Database: PDB / ID: 5umc
TitleSynthesis of novel seleno ureido containing compounds as SLC-0111 analogs. Investigations on carbonic anhydrases activity, glutathione peroxidase and X-ray crystallography
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic Anhydrase Inhibitors / Metalloenzymes / Glutathione Peroxidase
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 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
Unknown ligand / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPeat, T.S. / Angeli, A. / Tanini, D. / Bartolucci, G. / Capperucci, A. / 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
DepositionJan 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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)29,5395
Polymers29,2891
Non-polymers2504
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.485, 41.498, 72.280
Angle α, β, γ (deg.)90.00, 104.42, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 41.62 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: concentrated CA II at ~10 mg/mL was set up in SD-2 plates (Molecular Dimensions) with the following ratio of protein plus reservoir plus seeds: 250 nL + 225 nL + 25 nL. The plate was ...Details: concentrated CA II at ~10 mg/mL was set up in SD-2 plates (Molecular Dimensions) with the following ratio of protein plus reservoir plus seeds: 250 nL + 225 nL + 25 nL. The plate was incubated at 8 C and the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3. Dry compound was added to the crystallization drop after crystals had formed and several days before data were collected.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.15→41.5 Å / Num. obs: 13493 / % possible obs: 99.3 % / Redundancy: 5 % / CC1/2: 0.978 / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.112 / Net I/σ(I): 5.7
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2 / Num. unique obs: 1034 / CC1/2: 0.755 / Rpim(I) all: 0.396 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4cq0

4cq0


Resolution: 2.15→41.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.883 / SU B: 8.322 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26112 680 5 %RANDOM
Rwork0.19628 ---
obs0.19944 12801 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.219 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0 Å20.42 Å2
2---2.36 Å20 Å2
3---2.81 Å2
Refinement stepCycle: 1 / Resolution: 2.15→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 35 97 2191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192223
X-RAY DIFFRACTIONr_bond_other_d0.0060.022012
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9683016
X-RAY DIFFRACTIONr_angle_other_deg134698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9495266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79824.653101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08115365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.734157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
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_it1.3311.9541052
X-RAY DIFFRACTIONr_mcbond_other1.3281.9511051
X-RAY DIFFRACTIONr_mcangle_it2.1542.9251319
X-RAY DIFFRACTIONr_mcangle_other2.1552.9281320
X-RAY DIFFRACTIONr_scbond_it1.5732.1161171
X-RAY DIFFRACTIONr_scbond_other1.5752.1211168
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5643.11697
X-RAY DIFFRACTIONr_long_range_B_refined4.26936.3279373
X-RAY DIFFRACTIONr_long_range_B_other4.26936.3259374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.147→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 55 -
Rwork0.295 881 -
obs--92.22 %

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