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- PDB-6t9z: Nidocarborane inhibitor of Carbonic Anhydrase IX -

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Basic information

Entry
Database: PDB / ID: 6t9z
TitleNidocarborane inhibitor of Carbonic Anhydrase IX
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic Anhydrase IX / 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 / 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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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
Nidocarborane / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.12 Å
AuthorsBrynda, J. / Rezacova, P. / Kugler, M. / Gruner, B.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGA15-05677S Czech Republic
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Sulfonamido carboranes as highly selective inhibitors of cancer-specific carbonic anhydrase IX.
Authors: Dvoranova, J. / Kugler, M. / Holub, J. / Sicha, V. / Das, V. / Nekvinda, J. / El Anwar, S. / Havranek, M. / Pospisilova, K. / Fabry, M. / Kral, V. / Medvedikova, M. / Matejkova, S. / ...Authors: Dvoranova, J. / Kugler, M. / Holub, J. / Sicha, V. / Das, V. / Nekvinda, J. / El Anwar, S. / Havranek, M. / Pospisilova, K. / Fabry, M. / Kral, V. / Medvedikova, M. / Matejkova, S. / Liskova, B. / Gurska, S. / Dzubak, P. / Brynda, J. / Hajduch, M. / Gruner, B. / Rezacova, P.
History
DepositionOct 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)29,5884
Polymers29,2011
Non-polymers3873
Water5,008278
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint4 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.928, 41.239, 72.662
Angle α, β, γ (deg.)90.000, 104.020, 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-MYW / Nidocarborane


Mass: 243.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8B9NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 50 mM TRIS-HCl 1.6 M Sodium Citrat

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.12→35.6 Å / Num. obs: 85206 / % possible obs: 91.3 % / Redundancy: 2.57 % / Biso Wilson estimate: 10.963 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.045 / Χ2: 0.966 / Net I/σ(I): 17.98 / Num. measured all: 218966
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
1.12-1.192.5960.1386.73422715017131850.9650.17687.8
1.19-1.272.5950.1078.523373914140130020.9780.13692
1.27-1.372.5970.07811.513163813137121810.9870.09992.7
1.37-1.52.5860.05815.292926512100113160.9930.07493.5
1.5-1.682.5770.04121.072665010999103420.9960.05294
1.68-1.932.5670.03126.8123430966291290.9970.0494.5
1.93-2.372.5530.02633.5219915824978010.9980.03394.6
2.37-3.342.5030.02336.2515013640159980.9980.02993.7
3.34-35.62.260.02434.865089362622520.9970.03162.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T7U

6t7u


Resolution: 1.12→35.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.032
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1598 4292 5 %RANDOM
Rwork0.1435 ---
obs0.1444 81539 92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.19 Å2 / Biso mean: 11.209 Å2 / Biso min: 4.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.05 Å2
2---0.01 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.12→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 23 287 2329
Biso mean--14.35 21.38 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192250
X-RAY DIFFRACTIONr_bond_other_d00.022085
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9863148
X-RAY DIFFRACTIONr_angle_other_deg5.53934871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60225.05101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7715365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.219157
X-RAY DIFFRACTIONr_chiral_restr0.1050.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212571
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02508
X-RAY DIFFRACTIONr_rigid_bond_restr14.70532236
X-RAY DIFFRACTIONr_sphericity_free15.7775167
X-RAY DIFFRACTIONr_sphericity_bonded8.35552262
LS refinement shellResolution: 1.12→1.147 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.192 288 -
Rwork0.152 5472 -
obs--83.75 %

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