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- PDB-9f2n: Structure of human carbonic anhydrase XII complexed with 3-(cyclo... -

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Basic information

Entry
Database: PDB / ID: 9f2n
TitleStructure of human carbonic anhydrase XII complexed with 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5-(piperidin-1-yl)benzenesulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / DRUG DESIGN / CARBONIC ANHYDRASE / BENZENESULFONAMIDE
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: 1.21 Å
AuthorsManakova, E.N. / Grazulis, S. / Paketuryte, V. / Smirnov, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-Discovery871037European 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
DepositionApr 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,32311
Polymers59,8352
Non-polymers1,4889
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint13 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.093, 74.358, 75.846
Angle α, β, γ (deg.)90.00, 107.01, 90.00
Int Tables number4
Space group name H-MP1211

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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: 29917.318 Da / Num. of mol.: 2 / Fragment: Human Carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET31A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43570, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1H9A / 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5-(piperidin-1-yl)benzenesulfonamide / 3-(cyclooctylamino)-2,6-bis(fluoranyl)-4-(3-oxidanylpropylsulfonyl)-5-piperidin-1-yl-benzenesulfonamide


Mass: 523.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H35F2N3O5S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Ammonium Citrate pH 7.0 0.1M; Ammonium Sulfate 0.2M; PEG4000 26%
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.905 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 1.21→72.53 Å / Num. obs: 147538 / % possible obs: 97.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.442 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 1.04 / Net I/av σ(I): 2.6 / Net I/σ(I): 8.4
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3726 / CC1/2: 0.602 / R split: 0.7 / Rpim(I) all: 0.72 / Χ2: 1.17 / % possible all: 50.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSVERSION Jan 10, 2022 BUILT=20220220data reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→38.21 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.085 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18166 14636 9.9 %RANDOM
Rwork0.14322 ---
obs0.14706 132667 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.809 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0.25 Å2
2--0.77 Å20 Å2
3---0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.21→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 90 475 4726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124420
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.851.666026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2535528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59523.547234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9915675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0711516
X-RAY DIFFRACTIONr_chiral_restr0.120.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023470
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.422.2182092
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2863.3252614
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.4542.692328
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.27432.8276873
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.78334420
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.21→1.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 708 -
Rwork0.437 6146 -
obs--61.28 %

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