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- PDB-3d3p: Crystal structure of PDE4B catalytic domain in complex with a pyr... -

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Basic information

Entry
Database: PDB / ID: 3d3p
TitleCrystal structure of PDE4B catalytic domain in complex with a pyrazolopyridine inhibitor
ComponentscAMP-specific 3',5'-cyclic phosphodiesterase 4B
KeywordsHYDROLASE / PDE / PHOSPHODIESTERASE / cAMP / Alternative splicing / Phosphoprotein / Polymorphism
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 / regulation of cardiac muscle cell contraction / gamma-tubulin binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / leukocyte migration / voltage-gated calcium channel complex ...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 / regulation of cardiac muscle cell contraction / gamma-tubulin binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / leukocyte migration / voltage-gated calcium channel complex / cAMP catabolic process / calcium channel regulator activity / excitatory synapse / 3',5'-cyclic-AMP phosphodiesterase activity / DARPP-32 events / cAMP binding / cellular response to epinephrine stimulus / positive regulation of interleukin-2 production / neutrophil chemotaxis / Z disc / positive regulation of type II interferon production / cellular response to xenobiotic stimulus / synaptic vesicle / T cell receptor signaling pathway / cellular response to lipopolysaccharide / transmembrane transporter binding / dendritic spine / postsynaptic density / centrosome / perinuclear region of cytoplasm / signal transduction / 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-20A / ARSENIC / 3',5'-cyclic-AMP phosphodiesterase 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsSomers, D.O. / Neu, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Pyrazolopyridines as a novel structural class of potent and selective PDE4 inhibitors.
Authors: Hamblin, J.N. / Angell, T.D. / Ballantine, S.P. / Cook, C.M. / Cooper, A.W. / Dawson, J. / Delves, C.J. / Jones, P.S. / Lindvall, M. / Lucas, F.S. / Mitchell, C.J. / Neu, M.Y. / Ranshaw, L.E. ...Authors: Hamblin, J.N. / Angell, T.D. / Ballantine, S.P. / Cook, C.M. / Cooper, A.W. / Dawson, J. / Delves, C.J. / Jones, P.S. / Lindvall, M. / Lucas, F.S. / Mitchell, C.J. / Neu, M.Y. / Ranshaw, L.E. / Solanke, Y.E. / Somers, D.O. / Wiseman, J.O.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2787
Polymers40,5841
Non-polymers6946
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.448, 94.725, 105.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

21A-607-

HOH

31A-638-

HOH

41A-765-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein cAMP-specific 3',5'-cyclic phosphodiesterase 4B / DPDE4 / PDE32


Mass: 40583.949 Da / Num. of mol.: 1 / Fragment: Catalytic domain, residues 324-675 / Mutation: S654A, S659A, S661A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4B, DPDE4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q07343, 3',5'-cyclic-nucleotide phosphodiesterase

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Non-polymers , 5 types, 309 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-20A / 1-ethyl-N-(phenylmethyl)-4-(tetrahydro-2H-pyran-4-ylamino)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide / N-benzyl-1-ethyl-4-(tetrahydro-2H-pyran-4-ylamino)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide


Mass: 379.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N5O2
#5: Chemical ChemComp-ARS / ARSENIC / Arsenic


Mass: 74.922 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: As
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14-18% PEG 3000, 10% Glycerol, 50mM Sodium Cacodylate pH 6.5, 100mM Sodium Acetate, 1M Sodium Chloride, 1% DMF, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9326 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 44609 / % possible obs: 98.4 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.863 / Net I/σ(I): 10.9
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4351 / Χ2: 0.595 / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
AMoREphasing
RefinementStarting model: PDB ENTRY 1F0J (Molecule A)

1f0j


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.678 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2235 5 %RANDOM
Rwork0.199 ---
obs0.201 44290 100 %-
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 mean: 30.138 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å20 Å2
2---0.36 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 34 303 3051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212802
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9513802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9265337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19225140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41915491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.3571513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022114
X-RAY DIFFRACTIONr_nbd_refined0.2180.21458
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2290
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.215
X-RAY DIFFRACTIONr_mcbond_it2.04731732
X-RAY DIFFRACTIONr_mcangle_it2.81142726
X-RAY DIFFRACTIONr_scbond_it3.60551219
X-RAY DIFFRACTIONr_scangle_it5.10971075
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 156 -
Rwork0.265 3005 -
all-3161 -
obs--100 %

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