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- PDB-5tfx: New method for synthesis of benzoxazole amide inhibitors of carbo... -

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Basic information

Entry
Database: PDB / ID: 5tfx
TitleNew method for synthesis of benzoxazole amide inhibitors of carbonic anhydrase
ComponentsCarbonic anhydrase 2
KeywordsLyase/Lyase Inhibitor / carbonic anhydrase mimic / inhibitor / 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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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
N-(5-sulfamoyl-1,3-benzoxazol-2-yl)benzamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPeat, T.S. / Supuran, C.
CitationJournal: Org. Biomol. Chem. / Year: 2016
Title: Intramolecular oxidative deselenization of acylselenoureas: a facile synthesis of benzoxazole amides and carbonic anhydrase inhibitors.
Authors: Angeli, A. / Peat, T.S. / Bartolucci, G. / Nocentini, A. / Supuran, C.T. / Carta, F.
History
DepositionSep 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Oct 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
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)29,7644
Polymers29,2891
Non-polymers4753
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.583, 41.549, 72.298
Angle α, β, γ (deg.)90.00, 104.58, 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-7B1 / N-(5-sulfamoyl-1,3-benzoxazol-2-yl)benzamide


Mass: 317.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11N3O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 41.8 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 2.7 M ammonium sulfate, 100 mM Tris pH 8.3 with protein at 7 mg/mL

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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: 1.5→41.6 Å / Num. obs: 38190 / % possible obs: 96.4 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.8
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2 / CC1/2: 0.668 / % possible all: 66.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5flo

5flo


Resolution: 1.5→41.6 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.878 / SU B: 3.607 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24619 1769 4.7 %RANDOM
Rwork0.18661 ---
obs0.18944 36248 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.662 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å20.05 Å2
2---0.16 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.5→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 29 270 2358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192227
X-RAY DIFFRACTIONr_bond_other_d0.0030.022087
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9593031
X-RAY DIFFRACTIONr_angle_other_deg1.06434837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67524.554101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04715371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.825158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212563
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02529
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_it1.2781.1221072
X-RAY DIFFRACTIONr_mcbond_other1.2171.1211071
X-RAY DIFFRACTIONr_mcangle_it1.51.6871351
X-RAY DIFFRACTIONr_mcangle_other1.5181.6891352
X-RAY DIFFRACTIONr_scbond_it1.7011.3531155
X-RAY DIFFRACTIONr_scbond_other1.7021.3541154
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9591.9241680
X-RAY DIFFRACTIONr_long_range_B_refined2.22822.2039749
X-RAY DIFFRACTIONr_long_range_B_other2.22822.2029750
X-RAY DIFFRACTIONr_rigid_bond_restr2.68934314
X-RAY DIFFRACTIONr_sphericity_free19.278554
X-RAY DIFFRACTIONr_sphericity_bonded5.47154460
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 87 -
Rwork0.203 1964 -
obs--69.93 %

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