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- PDB-7k6k: Carbonic Anhydrase II complexed with 4-(2-(3-(3,5-dimethylphenyl)... -

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Basic information

Entry
Database: PDB / ID: 7k6k
TitleCarbonic Anhydrase II complexed with 4-(2-(3-(3,5-dimethylphenyl)ureido)ethylsulfonamido)benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Carbonic Anhydrase / CAII / CAIX inhibitor / Structure guided drug design / Structure activity relationship study / Breast Cancer / LYASE / LYASE-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 / cytoplasm / cytosol
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
Chem-VZ1 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.306 Å
AuthorsAndring, J.T. / Singh, S. / McKenna, R.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Handling drug-target selectivity: A study on ureido containing Carbonic Anhydrase inhibitors.
Authors: Akgul, O. / Singh, S. / Andring, J.T. / McKenna, R. / Selleri, S. / Carta, F. / Angeli, A. / Supuran, C.T.
History
DepositionSep 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,9515
Polymers29,2891
Non-polymers6624
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-4 kcal/mol
Surface area11600 Å2
Unit cell
Length a, b, c (Å)42.308, 41.386, 71.757
Angle α, β, γ (deg.)90.000, 104.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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 (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 177 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-VZ1 / 4-{[(2-{[(3,5-dimethylphenyl)carbamoyl]amino}ethyl)sulfonyl]amino}benzene-1-sulfonamide


Mass: 426.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N4O5S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 41.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 1.6M Sodium Citrate, 50mM Tris, pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9177 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9177 Å / Relative weight: 1
ReflectionResolution: 1.306→32.07 Å / Num. obs: 56680 / % possible obs: 96.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 10.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 19.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.31-1.333.50.508733921030.8340.3070.5992.472.8
7.15-32.076.20.03123943840.9990.0130.03451.898.4

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2097refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.306→23.814 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 2727 4.81 %
Rwork0.1805 53933 -
obs0.1811 56660 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.27 Å2 / Biso mean: 14.7727 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: final / Resolution: 1.306→23.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 39 173 2261
Biso mean--32.53 21.7 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122164
X-RAY DIFFRACTIONf_angle_d2.1652934
X-RAY DIFFRACTIONf_chiral_restr0.303300
X-RAY DIFFRACTIONf_plane_restr0.016378
X-RAY DIFFRACTIONf_dihedral_angle_d14.0361719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.306-1.32970.2251130.2731211672
1.3297-1.35530.27461240.2394237883
1.3553-1.3830.26361300.2224276894
1.383-1.4130.25361240.2159283597
1.413-1.44590.21691440.198288199
1.4459-1.4820.21051590.1934289098
1.482-1.52210.23161450.1872286298
1.5221-1.56690.22171560.1835287699
1.5669-1.61750.19781250.1842289099
1.6175-1.67530.19551490.176290299
1.6753-1.74230.19951470.1751292499
1.7423-1.82160.21541720.1731287099
1.8216-1.91760.20981470.17152938100
1.9176-2.03770.18851640.16972903100
2.0377-2.19490.16851570.17152959100
2.1949-2.41560.15771660.17742921100
2.4156-2.76470.21351530.19222958100
2.7647-3.48140.19031210.18273003100
3.4814-23.8140.16181310.16233059100

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