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- PDB-3g3n: PDE7A catalytic domain in complex with 3-(2,6-difluorophenyl)-2-(... -

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Basic information

Entry
Database: PDB / ID: 3g3n
TitlePDE7A catalytic domain in complex with 3-(2,6-difluorophenyl)-2-(methylthio)quinazolin-4(3H)-one
ComponentsHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A
KeywordsHYDROLASE / pde7 / crystal / inhibitor complex / Alternative splicing / cAMP / Phosphoprotein
Function / homology
Function and homology information


3',5'-cyclic-AMP phosphodiesterase / cAMP catabolic process / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / G alpha (s) signalling events / perinuclear region of cytoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-TC8 / High affinity 3',5'-cyclic-AMP phosphodiesterase 7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCastano, T. / Wang, H.
CitationJournal: Chemmedchem / Year: 2009
Title: Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors
Authors: Castano, T. / Wang, H. / Campillo, N.E. / Ballester, S. / Gonzalez-Garcia, C. / Hernandez, J. / Perez, C. / Cuenca, J. / Perez-Castillo, A. / Martinez, A. / Huertas, O. / Gelpi, J.L. / ...Authors: Castano, T. / Wang, H. / Campillo, N.E. / Ballester, S. / Gonzalez-Garcia, C. / Hernandez, J. / Perez, C. / Cuenca, J. / Perez-Castillo, A. / Martinez, A. / Huertas, O. / Gelpi, J.L. / Luque, F.J. / Ke, H. / Gil, C.
History
DepositionFeb 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2934
Polymers36,8991
Non-polymers3943
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.447, 115.447, 64.389
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A / HCP1 / TM22


Mass: 36899.133 Da / Num. of mol.: 1 / Fragment: catalytic domain residues 139-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE7A, PDE7A1 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q13946, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical ChemComp-TC8 / 3-(2,6-difluorophenyl)-2-(methylthio)quinazolin-4(3H)-one / 3-(2,6-difluorophenyl)-2-(methylsulfanyl)quinazolin-4(3H)-one


Mass: 304.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10F2N2OS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 277 K / pH: 7.5
Details: The protein drops contain 2 ul PDE7A1-IBMX and 2 ul well buffer of buffer 0.6 - 0.8 M (NH4)2SO4, 2.5 - 5 mM beta-mercaptoethanol, 10 mM EDTA, 0.1 M Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING ...Details: The protein drops contain 2 ul PDE7A1-IBMX and 2 ul well buffer of buffer 0.6 - 0.8 M (NH4)2SO4, 2.5 - 5 mM beta-mercaptoethanol, 10 mM EDTA, 0.1 M Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 18071 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 19.5 % / Rmerge(I) obs: 0.102
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.245 1780 RANDOM
Rwork0.21 --
obs0.21 18071 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.406 Å20 Å20 Å2
2--4.406 Å20 Å2
3----8.811 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2596 0 23 0 2619
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1871.5
X-RAY DIFFRACTIONc_mcangle_it1.9152
X-RAY DIFFRACTIONc_scbond_it2.0352
X-RAY DIFFRACTIONc_scangle_it2.9532.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3dna-rna_rep.param
X-RAY DIFFRACTION4tc243.param
X-RAY DIFFRACTION5ion.param

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