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- PDB-7p1a: Carbonic Anhydrase VII Sultam Based Inhibitors -

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Basic information

Entry
Database: PDB / ID: 7p1a
TitleCarbonic Anhydrase VII Sultam Based Inhibitors
ComponentsCarbonic anhydrase 7
KeywordsLYASE / CARBONIC ANHYDRASE VII / INHIBITOR
Function / homology
Function and homology information


positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase VII / 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
Chem-4IQ / Carbonic anhydrase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.58 Å
AuthorsD'Ambrosio, K. / De Simone, G.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Sultam based Carbonic Anhydrase VII inhibitors for the management of neuropathic pain.
Authors: Akgul, O. / Lucarini, E. / Mannelli, L.D.C. / Ghelardini, C. / D'Ambrosio, K. / Buonanno, M. / Monti, S.M. / De Simone, G. / Angeli, A. / Supuran, C.T. / Carta, F.
History
DepositionJul 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5074
Polymers30,9261
Non-polymers5813
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.870, 89.400, 44.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Carbonic anhydrase 7 / Carbonate dehydratase VII / Carbonic anhydrase VII / CA-VII


Mass: 30925.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P43166, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-4IQ / 4-[2-[4-[(4-methylphenyl)methyl]-1,1-bis(oxidanylidene)-1,2,4-thiadiazinan-2-yl]ethyl]benzenesulfonamide


Mass: 423.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% PEG 3350, 0.2 M Ammonium acetate, 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 PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 36884 / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.041 / Rrim(I) all: 0.142 / Χ2: 1.012 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6311.30.55617670.9510.1730.5830.996100
1.63-1.6611.40.51218500.9520.1590.5360.999100
1.66-1.6911.80.45118000.9630.1370.4711.004100
1.69-1.7211.60.38918220.9730.120.4081.021100
1.72-1.7611.10.34518140.9660.1080.3621.008100
1.76-1.812.10.30218180.9710.0910.3150.995100
1.8-1.8512.10.2718220.9780.0810.2821.017100
1.85-1.9120.24718100.9780.0750.2581.009100
1.9-1.9511.60.22218380.9810.0680.2320.986100
1.95-2.0211.70.19118260.9830.0580.20.991100
2.02-2.0912.10.17518330.9880.0520.1831.017100
2.09-2.1711.50.16518320.9820.050.1721.009100
2.17-2.2712.60.15418160.9840.0450.160.988100
2.27-2.3912.90.14418590.990.0420.150.983100
2.39-2.5412.40.13818450.9880.0410.1441.028100
2.54-2.7412.30.12818520.9910.0380.1331.028100
2.74-3.0112.10.11918720.9910.0360.1250.987100
3.01-3.4512.90.11518850.9930.0330.121.051100
3.45-4.34120.10518990.9930.0320.1091.088100
4.34-5011.50.10220240.9920.0310.1071.02699.8

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Processing

Software
NameVersionClassification
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.58→39.65 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2062 1095 3 %
Rwork0.1892 35303 -
obs-36398 98.1 %
Solvent computationBsol: 44.2765 Å2
Displacement parametersBiso max: 50.45 Å2 / Biso mean: 17.555 Å2 / Biso min: 4 Å2
Baniso -1Baniso -2Baniso -3
1--2.362 Å20 Å20 Å2
2--0.886 Å20 Å2
3---1.476 Å2
Refinement stepCycle: final / Resolution: 1.58→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 35 179 2265
Biso mean--19.39 28.33 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.414
X-RAY DIFFRACTIONc_mcbond_it1.3351.5
X-RAY DIFFRACTIONc_scbond_it2.0592
X-RAY DIFFRACTIONc_mcangle_it2.1812
X-RAY DIFFRACTIONc_scangle_it3.0572.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.640.1974780.19743191326989.7
1.64-1.70.22441150.20473420353597.2
1.7-1.780.2585990.19593479357898.1
1.78-1.870.20851200.18643482360298.4
1.87-1.990.22051000.18083535363598.9
1.99-2.140.21081190.18893539365899.6
2.14-2.360.20491210.19213594371599.7
2.36-2.70.23911070.20543591369899.8
2.7-3.40.20161160.18753667378399.9
3.4-39.650.18081200.18033805392599.9
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ion_patch.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6trtok.par
X-RAY DIFFRACTION7gliceroloCSD.param

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