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- PDB-6zr9: The crystal structure of the complex of hCAVII with 2-(4-benzhydr... -

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Basic information

Entry
Database: PDB / ID: 6zr9
TitleThe crystal structure of the complex of hCAVII with 2-(4-benzhydrylpiperazin-1-yl)-N-(4-sulfamoylphenyl)acetamide
ComponentsCarbonic anhydrase 7
KeywordsLYASE / CARBONIC ANHYDRASE VII / PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding ...positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / 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-QOZ / Carbonic anhydrase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsD'Ambrosio, K. / De Simone, G. / Di Fiore, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationMOLIM ONCOBRAIN LAB Italy
CitationJournal: New J.Chem. / Year: 2021
Title: The crystal structures of 2-(4-benzhydrylpiperazin-1-yl)-N-(4-sulfamoylphenyl)acetamide in complex with human carbonic anhydrase II and VII provide insights into selective CA inhibitor development
Authors: D'Ambrosio, K. / Di Fiore, A. / Buonanno, M. / Kumari, S. / Tiwari, M. / Supuran, C.T. / Mishra, C.B. / Monti, S.M. / De Simone, G.
History
DepositionJul 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)31,4563
Polymers30,9261
Non-polymers5302
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.810, 88.600, 44.290
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-QOZ / 2-[4-(diphenylmethyl)piperazin-1-yl]-~{N}-(4-sulfamoylphenyl)ethanamide


Mass: 464.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28N4O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: CCD / Date: Nov 29, 2017 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 16529 / % possible obs: 95.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.029 / Rrim(I) all: 0.061 / Χ2: 1.035 / Net I/σ(I): 16.9 / Num. measured all: 61105
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.091.80.3757390.6830.330.5031.00188
2.09-2.121.90.3537380.7310.3110.4730.88985.8
2.12-2.161.90.3167530.7860.2780.4230.90688.5
2.16-2.2120.2587550.8320.2180.34190.1
2.21-2.262.20.2557720.8410.2050.3291.09291
2.26-2.312.40.2217730.9080.1690.281.02791.8
2.31-2.372.60.2078010.9230.1510.2581.09794
2.37-2.432.90.1957960.930.1340.2391.07495.3
2.43-2.53.20.1828290.9440.1180.2181.06597.4
2.5-2.583.30.1538480.9570.0960.1821.07998.1
2.58-2.683.50.1388400.9670.0850.1631.06498.5
2.68-2.783.70.118620.9830.0650.1291.0699.8
2.78-2.914.20.0958450.9870.0520.1090.996100
2.91-3.064.90.0838540.9930.0410.0931.024100
3.06-3.255.40.0648520.9960.030.071.024100
3.25-3.515.40.0478740.9980.0220.0521.093100
3.51-3.865.40.0418770.9990.0190.0450.999100
3.86-4.425.40.0318850.9990.0140.034199.9
4.42-5.565.30.0269030.9990.0120.0291.03699.7
5.56-5050.02493310.0110.0261.0497.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→33.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2411 938 5.5 %
Rwork0.196 14857 -
obs-15795 92.3 %
Solvent computationBsol: 50.3413 Å2
Displacement parametersBiso max: 64 Å2 / Biso mean: 25.2641 Å2 / Biso min: 7.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.626 Å20 Å20 Å2
2--1.227 Å20 Å2
3----0.601 Å2
Refinement stepCycle: final / Resolution: 2.05→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 34 103 2188
Biso mean--28.09 28.71 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.486
X-RAY DIFFRACTIONc_mcbond_it1.4011.5
X-RAY DIFFRACTIONc_scbond_it2.0322
X-RAY DIFFRACTIONc_mcangle_it2.2912
X-RAY DIFFRACTIONc_scangle_it2.9112.5
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 (%)
2.05-2.120.3805780.27491203128176.6
2.12-2.210.3089900.23441285137581.7
2.21-2.310.2908760.22591346142284.1
2.31-2.430.2782900.21491415150590.1
2.43-2.580.299960.22051511160795
2.58-2.780.24961110.21031564167597.8
2.78-3.060.2881920.21271572166498.6
3.06-3.50.2433930.19611621171499.5
3.5-4.410.18821030.16411639174299.7
4.41-33.40.18421090.16821701181098.7
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 DIFFRACTION6ch19.param

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