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- PDB-6yol: Meta-Nidocarborane propyl-sulfonamide in complex with CA IX mimic -

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Basic information

Entry
Database: PDB / ID: 6yol
TitleMeta-Nidocarborane 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 / cyanamide hydratase activity / 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 / cyanamide hydratase activity / 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 / 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
Meta-Nidocarborane propyl-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 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)29,5103
Polymers29,2011
Non-polymers3092
Water4,846269
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 area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.032, 41.443, 72.703
Angle α, β, γ (deg.)90.000, 103.860, 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-P5T / Meta-Nidocarborane propyl-sulfonamide


Mass: 243.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8B9NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
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: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.14→35.74 Å / Num. obs: 82863 / % possible obs: 94.4 % / Redundancy: 3.687 % / Biso Wilson estimate: 18.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Χ2: 1.146 / Net I/σ(I): 9.74 / Num. measured all: 305485
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
1.14-1.213.4971.02214136114114118270.4931.20283.8
1.21-1.33.7370.6841.764716613273126230.7090.79895.1
1.3-1.43.7460.3933.194424512370118120.8890.45795.5
1.4-1.533.7010.2235.444069711367109960.9570.2696.7
1.53-1.723.8370.1249.6382901030899780.9840.14496.8
1.72-1.983.6640.07515.4532404913888430.9930.08796.8
1.98-2.423.7780.05123.4728627773675770.9960.0697.9
2.42-3.423.5520.04127.5320887603358810.9970.04997.5
3.42-35.743.550.03531.1711808341333260.9970.04197.5

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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: 1.15→35.74 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.581 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.035
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1705 2098 2.5 %RANDOM
Rwork0.1409 ---
obs0.1417 80691 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 57.14 Å2 / Biso mean: 18.945 Å2 / Biso min: 10.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å20.68 Å2
2---0.2 Å2-0 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 1.15→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 19 282 2310
Biso mean--25.42 29.98 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192197
X-RAY DIFFRACTIONr_bond_other_d0.0040.022019
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9823073
X-RAY DIFFRACTIONr_angle_other_deg1.37434709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79524.74297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4215350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.685157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212495
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02498
X-RAY DIFFRACTIONr_rigid_bond_restr3.33832194
X-RAY DIFFRACTIONr_sphericity_free22.688552
X-RAY DIFFRACTIONr_sphericity_bonded10.85152316
LS refinement shellResolution: 1.15→1.176 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.385 126 -
Rwork0.368 4856 -
obs--77.69 %

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