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- PDB-9r30: Three dimensional structure of human carbonic anhydrase IX in com... -

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Basic information

Entry
Database: PDB / ID: 9r30
TitleThree dimensional structure of human carbonic anhydrase IX in complex with sulfonamide
ComponentsCarbonic anhydrase
KeywordsLYASE / CA IX / CA 9 / CARBONIC ANHYDRASE IX / CARBONIC ANHYDRASE 9
Function / homology
Function and homology information


secretion / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLeitans, 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
B: Carbonic anhydrase
C: Carbonic anhydrase
D: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,61012
Polymers112,3584
Non-polymers2,2528
Water7,728429
1
A: Carbonic anhydrase
C: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3056
Polymers56,1792
Non-polymers1,1264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-9 kcal/mol
Surface area19700 Å2
MethodPISA
2
B: Carbonic anhydrase
D: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3056
Polymers56,1792
Non-polymers1,1264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-10 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.585, 152.585, 172.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Carbonic anhydrase


Mass: 28089.598 Da / Num. of mol.: 4 / Mutation: C41S, N213Q
Source method: isolated from a genetically manipulated source
Details: two dimers / Source: (gene. exp.) Homo sapiens (human) / Gene: CA9 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A2R9BYT1, 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-A1JC2 / 2,6-bis(fluoranyl)-4-methylsulfonyl-3,5-bis[(4-oxidanylcyclohexyl)amino]benzenesulfonamide


Mass: 497.577 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H29F2N3O6S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE)

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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: 2→47.98 Å / Num. obs: 101262 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 32.954 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 1.529 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5077

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.98 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.65 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20622 5430 5.4 %RANDOM
Rwork0.17402 ---
obs0.17577 95828 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.359 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å2-0 Å2
2--0.38 Å20 Å2
3----1.23 Å2
Refinement stepCycle: 1 / Resolution: 2→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7360 0 132 429 7921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127696
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167172
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.86610524
X-RAY DIFFRACTIONr_angle_other_deg0.5811.74116536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.235564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.111101144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.21152
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029196
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021764
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_it3.3793.5873820
X-RAY DIFFRACTIONr_mcbond_other3.3753.5873820
X-RAY DIFFRACTIONr_mcangle_it4.6596.4334768
X-RAY DIFFRACTIONr_mcangle_other4.6586.4334769
X-RAY DIFFRACTIONr_scbond_it4.6264.1083876
X-RAY DIFFRACTIONr_scbond_other4.6254.1093877
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7787.3585757
X-RAY DIFFRACTIONr_long_range_B_refined8.72136.948072
X-RAY DIFFRACTIONr_long_range_B_other8.70436.637999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 395 -
Rwork0.271 7134 -
obs--99.97 %

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