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- PDB-30xx: Crystal structure of hCA II in complex with an 1-Aryl-6,7-dimetho... -

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Basic information

Entry
Database: PDB / ID: 30xx
TitleCrystal structure of hCA II in complex with an 1-Aryl-6,7-dimethoxy-3,4-dihydroisoquinoline-2(1H)-sulfonamide inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLYASE / protein-inhibitor adduct / selective inhibitor / structure-based drug design
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / Developmental Lineage of Pancreatic Ductal Cells / carbonic anhydrase / regulation of intracellular pH ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / Developmental Lineage of Pancreatic Ductal Cells / carbonic anhydrase / regulation of intracellular pH / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / apical part of cell / extracellular exosome / zinc ion binding / plasma membrane / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsDi Fiore, A. / De Simone, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2026
Title: 1-Aryl-6,7-Dimethoxy-3,4-Dihydroisoquinoline-2(1H)-Sulfonamides as hCA XII Selective Inhibitors: Experimental and Theoretical Studies to Interrogate the Isoform Selectivity.
Authors: Ricci, F. / Di Fiore, A. / Angeli, A. / De Luca, L. / Mancuso, F. / Esposito, D. / De Simone, G. / Supuran, C.T. / Gitto, R.
History
DepositionMay 18, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0014
Polymers29,4771
Non-polymers5243
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.333, 41.383, 71.942
Angle α, β, γ (deg.)90.00, 104.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29477.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1J8Y / (1~{S})-1-(4-fluorophenyl)-6,7-dimethoxy-3,4-dihydro-1~{H}-isoquinoline-2-sulfonamide


Mass: 366.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19FN2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3 M sodium citrate and 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 82177 / % possible obs: 95.1 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.038 / Rrim(I) all: 0.094 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.15-1.1740.67238130.6780.8990.3720.7731.07689.4
1.17-1.194.40.61439270.7920.940.3240.6971.06891.8
1.19-1.214.70.60240120.8240.950.3020.6761.10592.1
1.21-1.244.80.52839880.860.9620.2630.5921.06793.2
1.24-1.275.30.50540050.9230.980.2380.5591.06693.5
1.27-1.35.10.48940090.8570.9610.2370.5461.08993.1
1.3-1.335.70.44440170.9140.9770.20.4881.09393.5
1.33-1.365.80.43940490.9340.9830.1960.4821.09394.5
1.36-1.45.80.37540760.9420.9850.1680.4121.0994.9
1.4-1.455.80.35341060.9460.9860.1580.3881.07294.9
1.45-1.56.30.30940950.9670.9920.1330.3371.07495.4
1.5-1.566.10.25940970.9660.9910.1120.2831.09795
1.56-1.636.60.20841490.9830.9960.0880.2261.00696.1
1.63-1.726.40.16641570.9890.9970.0710.1811.04896.8
1.72-1.836.10.12641910.9890.9970.0560.1381.01497
1.83-1.976.30.09542470.9930.9980.0410.1041.00397.4
1.97-2.166.30.07141710.9950.9990.030.0771.0996.8
2.16-2.486.50.0643080.9970.9990.0250.0651.09698.2
2.48-3.126.20.04943120.9970.9990.0210.0531.03198.9
3.12-506.20.03744480.99810.0160.0411.01899.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.15→41 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.02 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15897 1970 2.4 %RANDOM
Rwork0.13223 ---
obs0.13285 79780 95.16 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.927 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0.1 Å2
2---0.24 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.15→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 32 231 2335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132212
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171991
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.643010
X-RAY DIFFRACTIONr_angle_other_deg1.5691.5994659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9335270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32323.738107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.815365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.519157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
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_it2.1431.0591068
X-RAY DIFFRACTIONr_mcbond_other1.9821.0531067
X-RAY DIFFRACTIONr_mcangle_it2.5751.5971342
X-RAY DIFFRACTIONr_mcangle_other2.5741.6021343
X-RAY DIFFRACTIONr_scbond_it6.5651.4211144
X-RAY DIFFRACTIONr_scbond_other6.5721.4241145
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3441.9781669
X-RAY DIFFRACTIONr_long_range_B_refined4.3413.6852500
X-RAY DIFFRACTIONr_long_range_B_other4.31613.3652457
X-RAY DIFFRACTIONr_rigid_bond_restr10.82334203
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 125 -
Rwork0.272 5582 -
obs--90.14 %

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