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- PDB-9h81: human carbonic anhydrase I in complex with Sonepiprazole -

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Basic information

Entry
Database: PDB / ID: 9h81
Titlehuman carbonic anhydrase I in complex with Sonepiprazole
ComponentsCarbonic anhydrase 1
KeywordsLYASE / carbonic anhydrase I / sulfonamide / inhibitor / metalloenzyme / sonepiprazole
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / extracellular exosome / zinc ion binding / 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
: / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Structural Studies of the Dopamine D 4 Receptor Antagonist Sonepiprazole as an Inhibitor of Human Carbonic Anhydrases.
Authors: Angeli, A. / Ferraroni, M. / Capasso, C. / Supuran, C.T.
History
DepositionOct 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Carbonic anhydrase 1
BBB: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7466
Polymers57,8122
Non-polymers9344
Water1,49583
1
AAA: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3733
Polymers28,9061
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3733
Polymers28,9061
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.625, 71.232, 121.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28906.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00915, 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-A1IS9 / Sonepiprazole / 4-[4-[2-[(1S})-3,4-dihydro-1H-isochromen-1-yl]ethyl]piperazin-1-yl]benzenesulfonamide


Mass: 401.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% PEG4000, 0.2 M sodium acetate, 0.1 M Tris pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→61.5 Å / Num. obs: 23430 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.132 / Net I/σ(I): 13.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2262 / CC1/2: 0.943 / Rrim(I) all: 0.715 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→61.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.335 / SU ML: 0.195 / Cross valid method: NONE / ESU R: 0.405 / ESU R Free: 0.272
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2624 1108 4.756 %
Rwork0.1955 22188 -
all0.199 --
obs-23296 99.602 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.359 Å2
Baniso -1Baniso -2Baniso -3
1-0.006 Å20 Å20 Å2
2--0.171 Å2-0 Å2
3----0.177 Å2
Refinement stepCycle: LAST / Resolution: 2.35→61.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 58 83 4157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134199
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173708
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6325718
X-RAY DIFFRACTIONr_angle_other_deg1.2541.5948676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9635512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66523.725204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28215664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3771514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02855
X-RAY DIFFRACTIONr_nbd_refined0.1890.2721
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.23336
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21974
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2122
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.216
X-RAY DIFFRACTIONr_nbd_other0.2220.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.26
X-RAY DIFFRACTIONr_mcbond_it2.5553.5062048
X-RAY DIFFRACTIONr_mcbond_other2.5553.5092049
X-RAY DIFFRACTIONr_mcangle_it3.8075.2622559
X-RAY DIFFRACTIONr_mcangle_other3.8085.2572558
X-RAY DIFFRACTIONr_scbond_it3.1223.8832151
X-RAY DIFFRACTIONr_scbond_other3.1213.8852152
X-RAY DIFFRACTIONr_scangle_it4.9935.6663158
X-RAY DIFFRACTIONr_scangle_other4.9935.6683159
X-RAY DIFFRACTIONr_lrange_it7.89967.04517382
X-RAY DIFFRACTIONr_lrange_other7.89666.95917367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.328880.2491614X-RAY DIFFRACTION100
2.411-2.4770.289740.2511572X-RAY DIFFRACTION100
2.477-2.5490.433690.2381545X-RAY DIFFRACTION99.8762
2.549-2.6270.277790.2291496X-RAY DIFFRACTION100
2.627-2.7130.305790.2161440X-RAY DIFFRACTION99.9342
2.713-2.8080.335840.2281368X-RAY DIFFRACTION99.7938
2.808-2.9140.318650.2321355X-RAY DIFFRACTION99.6491
2.914-3.0330.345640.2241301X-RAY DIFFRACTION99.8537
3.033-3.1670.264610.2061253X-RAY DIFFRACTION99.5455
3.167-3.3220.291610.2011205X-RAY DIFFRACTION100
3.322-3.5010.258570.2141159X-RAY DIFFRACTION100
3.501-3.7130.27580.2121079X-RAY DIFFRACTION99.5622
3.713-3.9680.361410.1951039X-RAY DIFFRACTION98.9918
3.968-4.2850.215480.159950X-RAY DIFFRACTION98.7141
4.285-4.6920.198360.148883X-RAY DIFFRACTION98.7111
4.692-5.2430.166500.151790X-RAY DIFFRACTION98.2456
5.243-6.0490.185270.169720X-RAY DIFFRACTION99.2032
6.049-7.3950.259350.157610X-RAY DIFFRACTION99.2308
7.395-10.4030.147170.141510X-RAY DIFFRACTION99.6219
10.403-61.50.22150.219299X-RAY DIFFRACTION98.4326

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