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- PDB-3f8e: Coumarins are a novel class of suicide carbonic anhydrase inhibitors -

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Basic information

Entry
Database: PDB / ID: 3f8e
TitleCoumarins are a novel class of suicide carbonic anhydrase inhibitors
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase / inhibitors / Disease mutation / Metal-binding
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / : / Chem-TE1 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTemperini, C. / Maresca, A. / Scozzafava, A. / Supuran, C.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Non-Zinc Mediated Inhibition of Carbonic Anhydrases: Coumarins Are a New Class of Suicide Inhibitors
Authors: Maresca, A. / Temperini, C. / Vu, H. / Pham, N.B. / Poulsen, S.-A. / Scozzafava, A. / Quinn, R.J. / Supuran, C.T.
History
DepositionNov 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)30,1586
Polymers29,2891
Non-polymers8695
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.170, 41.600, 72.230
Angle α, β, γ (deg.)90.00, 104.62, 90.00
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 / Carbonic anhydrase II / CA-II / Carbonate dehydratase II / Carbonic anhydrase C / CAC


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: The protein was purchased from Sigma-Aldrich. / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 195 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-TE1 / (2Z)-3-{2-hydroxy-5-[(1S)-1-hydroxy-3-methylbutyl]-4-methoxyphenyl}prop-2-enoic acid


Mass: 280.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O5
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: Tris-HCl (pH 7.7-7.8), sodium 4-(hydroxymercury)benzoate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Jun 26, 2008
RadiationMonochromator: capillary / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 16699 / Num. obs: 16598 / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.095 / Net I/σ(I): 12.96
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1667

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Processing

Software
NameVersionClassification
CrysalisProOxford Diffraction2006data collection
AMoREphasing
REFMAC5.2.0019refinement
CrysalisProOxford Diffraction2006data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CA2

1ca2


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.876 / SU B: 5.48 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26846 816 4.9 %RANDOM
Rwork0.19874 ---
obs0.20222 15715 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.06 Å2
2--0.09 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 32 190 2261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222153
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9632927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26824.69498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4315357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.721157
X-RAY DIFFRACTIONr_chiral_restr0.090.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021660
X-RAY DIFFRACTIONr_nbd_refined0.2020.21061
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2194
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.220
X-RAY DIFFRACTIONr_mcbond_it0.5641.51324
X-RAY DIFFRACTIONr_mcangle_it0.94822082
X-RAY DIFFRACTIONr_scbond_it1.4893970
X-RAY DIFFRACTIONr_scangle_it2.2964.5840
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 61 -
Rwork0.234 1133 -
obs--100 %

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