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- PDB-5w6e: PDE1b complexed with compound 3S -

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Basic information

Entry
Database: PDB / ID: 5w6e
TitlePDE1b complexed with compound 3S
ComponentsCalcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
KeywordsHydrolase/Hydrolase Inhibitor / Phosphodiesterase / inhibitor / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / cellular response to macrophage colony-stimulating factor stimulus / serotonin metabolic process / dopamine catabolic process / cellular response to granulocyte macrophage colony-stimulating factor stimulus / Cam-PDE 1 activation / 3',5'-cyclic-nucleotide phosphodiesterase / cGMP effects / monocyte differentiation ...calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / cellular response to macrophage colony-stimulating factor stimulus / serotonin metabolic process / dopamine catabolic process / cellular response to granulocyte macrophage colony-stimulating factor stimulus / Cam-PDE 1 activation / 3',5'-cyclic-nucleotide phosphodiesterase / cGMP effects / monocyte differentiation / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / response to amphetamine / cAMP-mediated signaling / locomotory behavior / visual learning / G alpha (s) signalling events / calmodulin binding / neuronal cell body / metal ion binding / cytosol
Similarity search - Function
3'5'-cyclic nucleotide phosphodiesterase N-terminal / 3'5'-cyclic nucleotide phosphodiesterase N-terminal / 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 N-terminal / 3'5'-cyclic nucleotide phosphodiesterase N-terminal / 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-0NY / Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsVajdos, F.F.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of Potent and Selective Periphery-Restricted Quinazoline Inhibitors of the Cyclic Nucleotide Phosphodiesterase PDE1.
Authors: Humphrey, J.M. / Movsesian, M. / Am Ende, C.W. / Becker, S.L. / Chappie, T.A. / Jenkinson, S. / Liras, J.L. / Liras, S. / Orozco, C. / Pandit, J. / Vajdos, F.F. / Vandeput, F. / Yang, E. / Menniti, F.S.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5524
Polymers42,1351
Non-polymers4173
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.782, 88.782, 134.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B / Cam-PDE 1B / 63 kDa Cam-PDE


Mass: 42134.945 Da / Num. of mol.: 1 / Fragment: UNP residues 122-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE1B, PDE1B1, PDES1B / Production host: Escherichia coli (E. coli)
References: UniProt: Q01064, 3',5'-cyclic-nucleotide phosphodiesterase
#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-0NY / 7,8-dimethoxy-N-[(2S)-1-(3-methyl-1H-pyrazol-5-yl)propan-2-yl]quinazolin-4-amine


Mass: 327.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS-HCL, 0.2 M MGCL2, 125 UM 5-(5-BROMO-2-PROPOXYPHENYL)-3-PROPYL-1H-PYRAZOLO[4,3-D]PYRIMIDIN-7(6H)-ONE, 15% PEG 8000, PH 8.5, VAPOR DIFFUSION, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 343112 / % possible obs: 97.8 % / Redundancy: 8.11 % / Net I/σ(I): 23.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40.1 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.261 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 2116 5 %RANDOM
Rwork0.1804 ---
obs0.1817 40164 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.6 Å2 / Biso mean: 24.3 Å2 / Biso min: 12.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.03 Å2
Refinement stepCycle: final / Resolution: 1.9→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 26 305 2924
Biso mean--24.2 43.8 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222675
X-RAY DIFFRACTIONr_bond_other_d00.021766
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9443625
X-RAY DIFFRACTIONr_angle_other_deg0.87234308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6775319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67224.127126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09815469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5751514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022957
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02556
LS refinement shellResolution: 1.898→1.948 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 168 -
Rwork0.205 2856 -
all-3024 -
obs--96.89 %

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