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- PDB-3w5e: Crystal structure of phosphodiesterase 4B in complex with compound 31e -

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Basic information

Entry
Database: PDB / ID: 3w5e
TitleCrystal structure of phosphodiesterase 4B in complex with compound 31e
ComponentscAMP-specific 3',5'-cyclic phosphodiesterase 4B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / phosphodiesterase / COPD / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / gamma-tubulin binding / regulation of cardiac muscle cell contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / leukocyte migration ...negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / gamma-tubulin binding / regulation of cardiac muscle cell contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / leukocyte migration / cAMP catabolic process / excitatory synapse / DARPP-32 events / calcium channel regulator activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / cellular response to epinephrine stimulus / positive regulation of interleukin-2 production / cAMP-mediated signaling / neutrophil chemotaxis / Z disc / positive regulation of type II interferon production / synaptic vesicle / cellular response to xenobiotic stimulus / T cell receptor signaling pathway / cellular response to lipopolysaccharide / transmembrane transporter binding / dendritic spine / postsynaptic density / centrosome / perinuclear region of cytoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Phosphodiesterase 4 upstream conserved regions (UCR) / Phosphodiesterase 4 upstream conserved regions (UCR) / 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. ...Phosphodiesterase 4 upstream conserved regions (UCR) / Phosphodiesterase 4 upstream conserved regions (UCR) / 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-NVW / 3',5'-cyclic-AMP phosphodiesterase 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTakahashi, M. / Hanzawa, H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Identification of the fused bicyclic 4-amino-2-phenylpyrimidine derivatives as novel and potent PDE4 inhibitors
Authors: Goto, T. / Shiina, A. / Yoshino, T. / Mizukami, K. / Hirahara, K. / Suzuki, O. / Sogawa, Y. / Takahashi, T. / Mikkaichi, T. / Nakao, N. / Takahashi, M. / Hasegawa, M. / Sasaki, S.
History
DepositionJan 28, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr1_auth_asym_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_asym_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

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Assembly

Deposited unit
A: cAMP-specific 3',5'-cyclic phosphodiesterase 4B
B: cAMP-specific 3',5'-cyclic phosphodiesterase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8458
Polymers86,7052
Non-polymers1,1406
Water6,125340
1
A: cAMP-specific 3',5'-cyclic phosphodiesterase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9234
Polymers43,3531
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cAMP-specific 3',5'-cyclic phosphodiesterase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9234
Polymers43,3531
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.064, 158.190, 58.157
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 cAMP-specific 3',5'-cyclic phosphodiesterase 4B / DPDE4 / PDE32


Mass: 43352.656 Da / Num. of mol.: 2 / Fragment: UNP residues 324-700
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPDE4, PDE4B / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q07343, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical ChemComp-NVW / N-tert-butyl-2-{4-[(5,5-dioxido-2-phenyl-7,8-dihydro-6H-thiopyrano[3,2-d]pyrimidin-4-yl)amino]phenyl}acetamide


Mass: 464.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H28N4O3S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.15 Å3/Da / Density % sol: 42.8 % / Mosaicity: 1.274 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10-20% PEG 3350, 0.2-0.4M CaCl2, 0.1M Tris/HCl (pH8.0), vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 30568 / % possible obs: 88.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.116 / Χ2: 1.324 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.385.50.49129321.037186.3
2.38-2.485.50.43629251.052186.9
2.48-2.595.60.37929381.082186.8
2.59-2.735.50.329601.091186.9
2.73-2.95.50.24730181.175188.2
2.9-3.125.50.18529981.273187.8
3.12-3.445.50.12930291.306188.5
3.44-3.935.50.130471.629188.1
3.93-4.955.30.0831721.871190.7
4.95-505.10.06835491.681196.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f0j

1f0j


Resolution: 2.3→19.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.218 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.62 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 3026 10 %RANDOM
Rwork0.1819 ---
obs0.1904 30175 88.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 117.3 Å2 / Biso mean: 45.7954 Å2 / Biso min: 24.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 70 340 5994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025772
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9557828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3955686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79325.034290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.343151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9281526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024428
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 206 -
Rwork0.215 1761 -
all-1967 -
obs--85.63 %

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