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- PDB-9r31: Three dimensional structure of human carbonic anhydrase XII in co... -

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Basic information

Entry
Database: PDB / ID: 9r31
TitleThree dimensional structure of human carbonic anhydrase XII in complex with sulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / CA XII / CA 12 / CARBONIC ANHYDRASE XII / CARBONIC ANHYDRASE 12
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane
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
: / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsEimonta, V. / Leitans, J. / Tars, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)5.2.1.1.i.0/2/24/I/CFLA/001European Union
CitationJournal: J.Med.Chem. / Year: 2025
Title: Di- meta -Substituted Fluorinated Benzenesulfonamides as Potent and Selective Anticancer Inhibitors of Carbonic Anhydrase IX and XII.
Authors: Vaskevicius, A. / Zvirblis, M. / Kurtenoka, M. / Leitans, J. / Manakova, E. / Paketuryte-Latve, V. / Kvietkauskaite, A. / Kazaks, A. / Eimonta, V. / Cerepenkaite, K. / Kazokaite-Adomaitiene, ...Authors: Vaskevicius, A. / Zvirblis, M. / Kurtenoka, M. / Leitans, J. / Manakova, E. / Paketuryte-Latve, V. / Kvietkauskaite, A. / Kazaks, A. / Eimonta, V. / Cerepenkaite, K. / Kazokaite-Adomaitiene, J. / Mickeviciu̅te, A. / Juozapaitiene, V. / Tars, K. / Grazulis, S. / Matuliene, J. / Dudutiene, V. / Shubin, K. / Matulis, D. / Zubriene, A.
History
DepositionMay 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,39012
Polymers120,2464
Non-polymers2,1448
Water17,439968
1
A: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1956
Polymers60,1232
Non-polymers1,0724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 12
C: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1956
Polymers60,1232
Non-polymers1,0724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.617, 67.467, 80.859
Angle α, β, γ (deg.)81.17, 84.19, 86.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Carbonic anhydrase 12 / Carbonate dehydratase XII / Carbonic anhydrase XII / CA-XII / Tumor antigen HOM-RCC-3.1.3


Mass: 30061.447 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Production host: Escherichia coli (E. coli) / References: UniProt: O43570, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-A1H89 / 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5- methoxybenzenesulfonamide / 3-(cyclooctylamino)-2,6-bis(fluoranyl)-5-methoxy-4-(3-oxidanylpropylsulfonyl)benzenesulfonamide


Mass: 470.552 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H28F2N2O6S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 968 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.15 M MgCl2, 0.1 M NaAce (pH 5.5), 15% PEG 4000,PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS DISSOLVED IN 100% DMSO)

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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 PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2024
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.25→41.75 Å / Num. obs: 255967 / % possible obs: 95.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 7.081 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.8
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 12344

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→41.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.193 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21513 12831 5 %RANDOM
Rwork0.18477 ---
obs0.1863 243130 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.646 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-1.21 Å20.78 Å2
2---0.27 Å21.33 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.25→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 124 968 9428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0128716
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167734
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.83811890
X-RAY DIFFRACTIONr_angle_other_deg0.6751.7617887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.39451036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.624530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16101338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210226
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022034
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_it4.691.1714156
X-RAY DIFFRACTIONr_mcbond_other4.6891.1714156
X-RAY DIFFRACTIONr_mcangle_it6.7642.115188
X-RAY DIFFRACTIONr_mcangle_other6.7642.115189
X-RAY DIFFRACTIONr_scbond_it4.5211.2924560
X-RAY DIFFRACTIONr_scbond_other4.521.2924561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4322.3096703
X-RAY DIFFRACTIONr_long_range_B_refined12.63314.589732
X-RAY DIFFRACTIONr_long_range_B_other11.74913.579508
X-RAY DIFFRACTIONr_rigid_bond_restr4.602316450
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 924 -
Rwork0.216 17540 -
obs--93.05 %

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