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- PDB-6yo7: Ortho-Carborane di-propyl-sulfonamide in complex with CA IX mimic -

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Basic information

Entry
Database: PDB / ID: 6yo7
TitleOrtho-Carborane di-propyl-sulfonamide in complex with CA IX mimic
ComponentsCarbonic anhydrase 2
KeywordsLYASE / CARBONIC ANHYDRASE / CA INHIBITOR
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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / 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
Ortho-Carborane di-propyl-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.17 Å
AuthorsKugler, M. / Brynda, J. / Pospisilova, K. / Rezacova, P.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science FoundationGA15-05677S Czech Republic
Other governmentTE01020028 Czech Republic
CitationJournal: Chemistry / Year: 2020
Title: Direct Introduction of an Alkylsulfonamido Group on C-sites of Isomeric Dicarba-closo-dodecaboranes: The Influence of Stereochemistry on Inhibitory Activity against the Cancer-Associated ...Title: Direct Introduction of an Alkylsulfonamido Group on C-sites of Isomeric Dicarba-closo-dodecaboranes: The Influence of Stereochemistry on Inhibitory Activity against the Cancer-Associated Carbonic Anhydrase IX Isoenzyme.
Authors: Nekvinda, J. / Kugler, M. / Holub, J. / El Anwar, S. / Brynda, J. / Pospisilova, K. / Ruzickova, Z. / Rezacova, P. / Gruner, B.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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)29,6433
Polymers29,2011
Non-polymers4422
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.719, 41.033, 71.716
Angle α, β, γ (deg.)90.000, 103.700, 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: 29200.887 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-P7Z / Ortho-Carborane di-propyl-sulfonamide


Mass: 376.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16B10N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris-H2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.17→35.36 Å / Num. obs: 75212 / % possible obs: 94.2 % / Redundancy: 3.525 % / Biso Wilson estimate: 17.258 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.057 / Χ2: 0.844 / Net I/σ(I): 12.05 / Num. measured all: 265129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.17-1.242.4640.8091.01229881283893280.5161.03572.7
1.24-1.333.4770.6491.714059112049116730.9150.7796.9
1.33-1.433.6270.4472.614016211260110740.8480.52598.3
1.43-1.573.7970.2644.553892810340102510.9420.30899.1
1.57-1.753.6550.1437.9633925939592830.980.16898.8
1.75-2.023.8410.0716.1831504828882030.9950.08299
2.02-2.483.730.0428.3825983704869660.9980.04798.8
2.48-3.53.6890.02641.7319847548053800.9990.03198.2
3.5-35.363.6680.0256.4711201310930540.9990.02398.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5OGP

5ogp


Resolution: 1.17→35.36 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.143 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.04
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1848 2100 2.8 %RANDOM
Rwork0.1597 ---
obs0.1604 73111 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.45 Å2 / Biso mean: 16.799 Å2 / Biso min: 7.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å2-0 Å2-0.76 Å2
2--0.62 Å20 Å2
3---1.28 Å2
Refinement stepCycle: final / Resolution: 1.17→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 27 236 2271
Biso mean--21.24 28.39 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192210
X-RAY DIFFRACTIONr_bond_other_d0.0050.022020
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9953123
X-RAY DIFFRACTIONr_angle_other_deg4.35734709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8675284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83924.84899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06115342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.62157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212509
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02500
X-RAY DIFFRACTIONr_rigid_bond_restr21.45332191
X-RAY DIFFRACTIONr_sphericity_free21.189554
X-RAY DIFFRACTIONr_sphericity_bonded12.46152270
LS refinement shellResolution: 1.17→1.2 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.378 104 -
Rwork0.343 3624 -
obs--63.67 %

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