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- PDB-8vq6: hCA-II-4-(2-Aminoethyl)benzenesulfonamide-complex. Two molecules ... -

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Basic information

Entry
Database: PDB / ID: 8vq6
TitlehCA-II-4-(2-Aminoethyl)benzenesulfonamide-complex. Two molecules of inhibitor bound to active site and secondary binding pocket
ComponentsCarbonic anhydrase 2
KeywordsLYASE/INHIBITOR / Carbonic Anhydrase II / human Carbonic anhydrase II / carbon anhydrase / Two pockets bound / binding pocket / binding pockets / active site / small molecule / bivalent / complex / protein ligand complex / protein inhibition / inhibitor / binder / nano molar binder / nano molar inhibitor / PROTEIN BINDING / 4-(2-Aminoethyl)benzenesulfonamide / secondary binding site / ZYX / LYASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / 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
4-(2-AMINOETHYL)BENZENESULFONAMIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsIsmail, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: SBDD of Carbonic Anhydrase II Inhibitors
Authors: Ismail, M.M.
History
DepositionJan 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: 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)29,9555
Polymers29,2891
Non-polymers6664
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.547, 41.376, 72.679
Angle α, β, γ (deg.)90.000, 104.566, 90.000
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: 29289.062 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 BL21(DE3) (bacteria) / 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-ZYX / 4-(2-AMINOETHYL)BENZENESULFONAMIDE / P-AMINOETHYL BENZENESULFONAMIDE


Mass: 200.258 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H12N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.5 M NaCit, 0.1 M Tris, pH 8.5 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→70.343 Å / Num. obs: 43063 / % possible obs: 98.6 % / Redundancy: 4.4 % / CC1/2: 0.666 / Rmerge(I) obs: 0.399 / Rpim(I) all: 0.234 / Rrim(I) all: 0.467 / Net I/σ(I): 7
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2100 / CC1/2: 0.105 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→70.343 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.866 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1894 2040 4.745 %
Rwork0.1605 40950 -
all0.162 --
obs-42990 98.4 %
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: 7.685 Å2
Baniso -1Baniso -2Baniso -3
1-0.897 Å2-0 Å2-1.077 Å2
2--1.437 Å20 Å2
3----1.563 Å2
Refinement stepCycle: LAST / Resolution: 1.45→70.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 40 247 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122243
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162071
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.6423064
X-RAY DIFFRACTIONr_angle_other_deg1.1061.6124815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.48558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39610373
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.30610105
X-RAY DIFFRACTIONr_chiral_restr0.1030.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022665
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02505
X-RAY DIFFRACTIONr_nbd_refined0.1990.2408
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21898
X-RAY DIFFRACTIONr_nbtor_refined0.180.21056
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2170
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0840.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.220
X-RAY DIFFRACTIONr_nbd_other0.2350.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.250.222
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0210.21
X-RAY DIFFRACTIONr_mcbond_it0.4810.6811069
X-RAY DIFFRACTIONr_mcbond_other0.480.681069
X-RAY DIFFRACTIONr_mcangle_it0.7231.2241348
X-RAY DIFFRACTIONr_mcangle_other0.7231.2261349
X-RAY DIFFRACTIONr_scbond_it0.5590.8261174
X-RAY DIFFRACTIONr_scbond_other0.5590.8271175
X-RAY DIFFRACTIONr_scangle_it0.7931.4381710
X-RAY DIFFRACTIONr_scangle_other0.7931.4381711
X-RAY DIFFRACTIONr_lrange_it2.4079.4242557
X-RAY DIFFRACTIONr_lrange_other2.2569.4282549
X-RAY DIFFRACTIONr_rigid_bond_restr4.33434314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.45-1.4870.2381460.21329120.21532220.9720.97494.910.166
1.487-1.5280.2431480.19329080.19531280.9630.97997.69820.152
1.528-1.5720.2021380.17528130.17730300.9770.98397.39270.143
1.572-1.6210.1721490.17127400.17129400.9810.98498.26530.145
1.621-1.6740.2061370.16726570.16928510.9730.98398.00070.145
1.674-1.7330.1911340.16326140.16427990.9780.98598.17790.145
1.733-1.7980.231180.16225280.16526850.9640.98498.54750.15
1.798-1.8710.1921070.15324060.15425540.9720.98698.39470.142
1.871-1.9550.173840.14923650.1524940.9820.98798.19570.145
1.955-2.050.178990.15122270.15223550.980.98798.76860.156
2.05-2.1610.171100.1421410.14222640.9820.98999.42580.148
2.161-2.2920.1681090.13620210.13821400.9830.98999.53270.147
2.292-2.450.183970.14419090.14620110.9810.98799.75140.161
2.45-2.6460.1821050.15117560.15218670.9820.98699.67860.171
2.646-2.8980.189800.16316400.16417270.9770.98399.59470.19
2.898-3.2390.21760.16314850.16515730.970.98399.23710.19
3.239-3.7390.195600.16313250.16413950.9760.98399.28310.196
3.739-4.5760.136660.14111190.1411860.9920.98799.91570.172
4.576-6.4580.222490.1828720.1849220.9750.98399.89150.227
6.458-70.3430.197280.2185110.2175390.9810.9651000.272

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