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- PDB-9f3g: Human carbonic anhydrase XII with 3-(cyclooctylamino)-2,6-difluor... -

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Basic information

Entry
Database: PDB / ID: 9f3g
TitleHuman carbonic anhydrase XII with 3-(cyclooctylamino)-2,6-difluoro-5-((4-hydroxybutyl)amino)-4-((3-hydroxypropyl)sulfonyl)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. / Grazulis, S. / Smirnov, A. / Paketuryte, V.
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 25, 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
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,19130
Polymers119,6694
Non-polymers3,52226
Water20,2671125
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,59515
Polymers59,8352
Non-polymers1,76113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,59515
Polymers59,8352
Non-polymers1,76113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.501, 74.116, 91.632
Angle α, β, γ (deg.)90.00, 108.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4 / Fragment: Human Carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: O43570, carbonic anhydrase

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Non-polymers , 5 types, 1151 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-A1H91 / 3-(cyclooctylamino)-2,6-bis(fluoranyl)-5-(4-oxidanylbutylamino)-4-[(~{E})-3-oxidanylprop-1-enyl]sulfonyl-benzenesulfonamide


Mass: 527.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H35F2N3O6S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1125 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Ammonium Citrate pH7.0 0.1M; Ammonium Sulfate 0.2M; PEG4000 26%

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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→86.73 Å / Num. obs: 290166 / % possible obs: 97 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.904 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.016 / Rrim(I) all: 0.043 / Χ2: 1.01 / Net I/av σ(I): 8.1 / Net I/σ(I): 18.6
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6944 / CC1/2: 0.719 / Rpim(I) all: 0.437 / Rrim(I) all: 0.698 / Χ2: 1.03 / % possible all: 46.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→86.73 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16764 29100 10 %RANDOM
Rwork0.13691 ---
obs0.13996 261008 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.266 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.16 Å2
2---0.52 Å20 Å2
3---0.49 Å2
Refinement stepCycle: 1 / Resolution: 1.21→86.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8395 0 212 1125 9732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129322
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.65912751
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05251155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48123.667499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.132151456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.981535
X-RAY DIFFRACTIONr_chiral_restr0.1040.21150
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027437
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_it2.4231.8964415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9362.8565587
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8032.3184907
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.54228.64614736
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.50339322
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.21→1.24 Å
RfactorNum. reflection% reflection
Rfree0.281 1385 -
Rwork0.272 12227 -
obs--61.76 %

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