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- PDB-8vq5: hCA-II-Bivalent compound bound complex EthylUreadibenzensulfonamide -

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Basic information

Entry
Database: PDB / ID: 8vq5
TitlehCA-II-Bivalent compound bound complex EthylUreadibenzensulfonamide
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 / urea / complex / protein ligand complex / protein inhibition / inhibitor / binder / nano molar binder / nano molar inhibitor / PROTEIN BINDING / 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 / cyanamide hydratase activity / 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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / 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: 1.5 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8524
Polymers29,1601
Non-polymers6923
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.420, 41.300, 72.500
Angle α, β, γ (deg.)90.000, 104.600, 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 / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 29159.883 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, cyanamide hydratase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1ADH / 4,4'-[carbonylbis(azanediylethane-2,1-diyl)]di(benzene-1-sulfonamide)


Mass: 426.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N4O5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZYX / 4-(2-AMINOETHYL)BENZENESULFONAMIDE / P-AMINOETHYL BENZENESULFONAMIDE


Mass: 200.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 41.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.1 M Malonate, Tris, pH 8.5 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 77 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.33→29.11 Å / Num. obs: 38694 / % possible obs: 69.8 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.033 / Rrim(I) all: 0.07 / Net I/σ(I): 12.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.03 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1400 / CC1/2: 0.921 / Rpim(I) all: 0.181 / % possible all: 55.35

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.11 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.528 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.159 1683 4.799 %
Rwork0.1239 33390 -
all0.126 --
obs-35073 89.445 %
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: 19.189 Å2
Baniso -1Baniso -2Baniso -3
1-0.518 Å2-0 Å22.951 Å2
2---2.988 Å2-0 Å2
3---0.822 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 42 221 2326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122207
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162028
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.6433006
X-RAY DIFFRACTIONr_angle_other_deg0.6011.6114706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.61657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43210362
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.93510101
X-RAY DIFFRACTIONr_chiral_restr0.1010.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022598
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02500
X-RAY DIFFRACTIONr_nbd_refined0.1980.2373
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21827
X-RAY DIFFRACTIONr_nbtor_refined0.180.21038
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21080
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2148
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2670.210
X-RAY DIFFRACTIONr_nbd_other0.2260.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2320.226
X-RAY DIFFRACTIONr_mcbond_it1.2471.8251050
X-RAY DIFFRACTIONr_mcbond_other1.241.8251050
X-RAY DIFFRACTIONr_mcangle_it1.6343.2981315
X-RAY DIFFRACTIONr_mcangle_other1.6343.2991316
X-RAY DIFFRACTIONr_scbond_it1.7332.1471157
X-RAY DIFFRACTIONr_scbond_other1.7322.1481158
X-RAY DIFFRACTIONr_scangle_it2.2173.7871686
X-RAY DIFFRACTIONr_scangle_other2.2163.7881687
X-RAY DIFFRACTIONr_lrange_it3.25622.8072460
X-RAY DIFFRACTIONr_lrange_other3.25722.7972458
X-RAY DIFFRACTIONr_rigid_bond_restr5.50234235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.237650.1931400X-RAY DIFFRACTION50.587
1.539-1.5810.234930.1731556X-RAY DIFFRACTION58.935
1.581-1.6270.196850.1541833X-RAY DIFFRACTION71.1953
1.627-1.6760.1931010.1372133X-RAY DIFFRACTION84.1748
1.676-1.7310.2021210.1232396X-RAY DIFFRACTION98.2052
1.731-1.7920.1331010.1062397X-RAY DIFFRACTION99.5219
1.792-1.8590.17960.0952270X-RAY DIFFRACTION98.7891
1.859-1.9350.1471000.12144X-RAY DIFFRACTION97.8204
1.935-2.020.1711110.1082099X-RAY DIFFRACTION98.8372
2.02-2.1190.1581260.1091981X-RAY DIFFRACTION99.5276
2.119-2.2320.131940.1051908X-RAY DIFFRACTION99.602
2.232-2.3670.146920.1041763X-RAY DIFFRACTION97.0188
2.367-2.5290.16980.1211699X-RAY DIFFRACTION99.7225
2.529-2.730.136590.1211609X-RAY DIFFRACTION99.5821
2.73-2.9880.181760.1271469X-RAY DIFFRACTION98.7852
2.988-3.3360.139650.1291317X-RAY DIFFRACTION98.363
3.336-3.8440.152540.1211183X-RAY DIFFRACTION98.8019
3.844-4.6880.147630.123981X-RAY DIFFRACTION97.8444
4.688-6.5450.152550.152791X-RAY DIFFRACTION100
6.545-29.110.189280.198456X-RAY DIFFRACTION96.4143

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