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- PDB-9yud: Re-Refined Human Phosphodiesterase 3B complexed with GSK4394835A -

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Basic information

Entry
Database: PDB / ID: 9yud
TitleRe-Refined Human Phosphodiesterase 3B complexed with GSK4394835A
ComponentscGMP-inhibited 3',5'-cyclic phosphodiesterase 3B
KeywordsHYDROLASE / phosphodiesterase / inhibitor / covalent / boronate
Function / homology
Function and homology information


PDE3B signalling / protein kinase B binding / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor complex / negative regulation of cell adhesion / negative regulation of cell adhesion mediated by integrin / 3',5'-cyclic-nucleotide phosphodiesterase / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity ...PDE3B signalling / protein kinase B binding / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor complex / negative regulation of cell adhesion / negative regulation of cell adhesion mediated by integrin / 3',5'-cyclic-nucleotide phosphodiesterase / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / negative regulation of cAMP/PKA signal transduction / regulation of angiogenesis / negative regulation of lipid catabolic process / negative regulation of angiogenesis / insulin receptor signaling pathway / angiogenesis / G alpha (s) signalling events / G protein-coupled receptor signaling pathway / endoplasmic reticulum / Golgi apparatus / metal ion binding / membrane / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
: / cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEaton, S.A. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery and SAR Study of Boronic Acid-Based Selective PDE3B Inhibitors from a Novel DNA-Encoded Library.
Authors: Rowley, A.M. / Yao, G. / Andrews, L. / Bedermann, A. / Biddulph, R. / Bingham, R. / Brady, J.J. / Buxton, R. / Cecconie, T. / Cooper, R. / Csakai, A. / Gao, E.N. / Grenier-Davies, M.C. / ...Authors: Rowley, A.M. / Yao, G. / Andrews, L. / Bedermann, A. / Biddulph, R. / Bingham, R. / Brady, J.J. / Buxton, R. / Cecconie, T. / Cooper, R. / Csakai, A. / Gao, E.N. / Grenier-Davies, M.C. / Lawler, M. / Lian, Y. / Macina, J. / Macphee, C. / Marcaurelle, L. / Martin, J. / McCormick, P. / Pindoria, R. / Rauch, M. / Rocque, W. / Shen, Y. / Shewchuk, L.M. / Squire, M. / Stebbeds, W. / Tear, W. / Wang, X. / Ward, P. / Xiao, S.
History
DepositionOct 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Remark 0THIS ENTRY 9YUD REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 8SYC, DETERMINED BY A.M.ROWLEY et al.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B
B: cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7057
Polymers102,1092
Non-polymers5965
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.586, 78.586, 166.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B / CGIPDE1 / CGIP1 / Cyclic GMP-inhibited phosphodiesterase B / CGI-PDE B


Mass: 51054.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE3B / Production host: Escherichia coli (E. coli)
References: UniProt: Q13370, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical ChemComp-X5W / [3-[(4,7-dimethoxyquinolin-2-yl)carbonylamino]-5-[methyl-(phenylmethyl)carbamoyl]phenyl]-oxidanyl-oxidanylidene-boron


Mass: 498.315 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C27H25BN3O6 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.52 Å3/Da / Density % sol: 51.1 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 8SYC.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M NaCl, 25%PEG3350,0.1 M bis-Tris pH 6.5, cryo: 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.68→71.16 Å / Num. obs: 18157 / % possible obs: 92.7 % / Redundancy: 4.8 % / CC1/2: 0.986 / Net I/σ(I): 6.8
Reflection shellResolution: 2.68→3.022 Å / Rmerge(I) obs: 1.648 / Num. unique obs: 312

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(1.19.2-4158)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→71.06 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 840 4.63 %
Rwork0.1868 --
obs0.1892 18141 65.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→71.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5441 0 41 45 5527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025633
X-RAY DIFFRACTIONf_angle_d0.4737709
X-RAY DIFFRACTIONf_dihedral_angle_d12.7551882
X-RAY DIFFRACTIONf_chiral_restr0.037854
X-RAY DIFFRACTIONf_plane_restr0.004997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.870.4357120.3064312X-RAY DIFFRACTION7
2.87-3.090.3315310.2915897X-RAY DIFFRACTION20
3.09-3.40.28411340.25132910X-RAY DIFFRACTION66
3.4-3.90.27612170.19144383X-RAY DIFFRACTION100
3.9-4.910.21982270.16484382X-RAY DIFFRACTION100
4.91-71.060.21092190.17444417X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.55982.65492.6764.80432.04033.19230.0442-0.34950.2309-0.075-0.13660.9139-0.5081-0.68720.45670.49330.1540.10740.5142-0.08570.3746-65.939850.23433.9186
22.63641.45330.08333.3321-0.34372.02190.1526-0.20450.3190.10610.00210.3877-0.5316-0.2755-0.15320.37080.15450.01970.38590.03780.2931-57.120145.70686.3047
33.75731.7161-0.98074.8029-2.13121.4609-0.041-0.6913-0.58110.671-0.17140.1701-1.5918-0.7396-0.3080.40840.099-0.03780.5539-0.02890.237-55.414943.444717.1007
43.2685-0.4554-1.78996.07481.97162.49290.0388-0.3668-0.7679-0.75720.05870.18330.1711-0.38780.23680.06940.05350.00320.5583-0.05820.2113-47.384330.9763-9.9816
52.24190.133-0.25656.05832.84452.99110.1534-0.10570.3715-0.1880.1026-0.5994-0.3990.3781-0.29010.3306-0.02240.00840.30150.00080.3004-43.554945.712.1361
60.96760.1368-0.45471.70511.4413.10120.1324-0.1663-0.0320.2337-0.0044-0.1274-0.4607-0.2693-0.12950.2299-0.0427-0.01360.39860.00330.2992-56.965829.7345.8184
71.20111.2532-1.09341.73741.37676.90050.254-0.0462-0.02450.1118-0.39620.07520.97-1.16790.08560.3626-0.0488-0.03030.40040.02580.3331-63.013622.2261-2.3005
80.665-1.2029-0.26163.24582.17975.21670.085-0.84-0.18440.2938-0.44450.61540.0146-0.69630.43770.3965-0.05280.09060.7811-0.04090.3736-71.565126.690512.1895
92.86310.0804-0.160.98-0.49272.61280.32140.84-0.2466-0.3775-0.0402-0.36670.22040.7423-0.23350.32550.00860.03270.798-0.21550.4213-16.37619.4091-14.1332
105.6729-2.05352.50643.46793.26847.59371.1295-0.1031-1.16650.93650.4-1.10930.26730.3175-0.96090.71610.2057-0.24430.4751-0.23930.791-22.13852.0533-4.6702
113.48390.90861.39787.7349-3.04365.85210.62540.3956-0.6732-0.0237-0.49290.20391.04270.3332-0.21160.48690.0039-0.04480.4196-0.17570.418-23.29528.0566-5.5031
123.17590.39462.05865.42492.68523.95190.01230.5057-0.0088-0.5283-0.109-0.0473-0.28790.3190.0820.253-0.05910.03850.3797-0.01350.2604-30.954131.4167-9.9031
132.93953.5757-0.10177.22340.21044.96380.4730.706-0.0291-0.1105-0.17421.28010.23-0.3449-0.15040.29840.0173-0.1450.396-0.2970.4191-35.484518.9054-8.4783
148.60473.43742.23525.26712.56013.42040.4391-0.8747-1.17011.5331-0.2877-0.83110.6685-0.161-0.17250.3584-0.02930.09530.4883-0.09560.4853-30.214714.96759.7635
152.4951-0.76270.10273.6339-0.10752.34970.18380.13790.04570.2226-0.0005-0.228-0.24470.4438-0.1960.3045-0.1230.05120.4787-0.10510.2359-16.785329.78614.6053
165.9217-1.46681.39360.85020.65773.70360.73990.0988-0.88821.30290.2389-1.34860.57070.5539-0.84440.51620.0322-0.13440.5293-0.16670.5936-9.078117.147110.4144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 664 through 707 )
2X-RAY DIFFRACTION2chain 'A' and (resid 708 through 792 )
3X-RAY DIFFRACTION3chain 'A' and (resid 793 through 820 )
4X-RAY DIFFRACTION4chain 'A' and (resid 821 through 848 )
5X-RAY DIFFRACTION5chain 'A' and (resid 849 through 893 )
6X-RAY DIFFRACTION6chain 'A' and (resid 894 through 968 )
7X-RAY DIFFRACTION7chain 'A' and (resid 969 through 1005 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1006 through 1078 )
9X-RAY DIFFRACTION9chain 'B' and (resid 666 through 754 )
10X-RAY DIFFRACTION10chain 'B' and (resid 755 through 791 )
11X-RAY DIFFRACTION11chain 'B' and (resid 792 through 820 )
12X-RAY DIFFRACTION12chain 'B' and (resid 821 through 875 )
13X-RAY DIFFRACTION13chain 'B' and (resid 876 through 893 )
14X-RAY DIFFRACTION14chain 'B' and (resid 894 through 921 )
15X-RAY DIFFRACTION15chain 'B' and (resid 922 through 1005 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1006 through 1079 )

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