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- PDB-5oy4: GSK3beta complex with N-(6-(3,4-dihydroxyphenyl)-1H-pyrazolo[3,4-... -

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Basic information

Entry
Database: PDB / ID: 5oy4
TitleGSK3beta complex with N-(6-(3,4-dihydroxyphenyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)acetamide
Components
  • Glycogen synthase kinase-3 beta
  • Proto-oncogene FRAT1
KeywordsTRANSFERASE / Phosphoinositide-3-kinase delta inhibitor / PI3K delta inhibitor / kinase cross-screening
Function / homology
Function and homology information


negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation ...negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / negative regulation of protein acetylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / tau-protein kinase / regulation of microtubule-based process / CRMPs in Sema3A signaling / regulation of protein export from nucleus / heart valve development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Maturation of nucleoprotein / cellular response to interleukin-3 / Wnt signalosome / regulation of axon extension / regulation of long-term synaptic potentiation / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / dopamine receptor signaling pathway / regulation of dendrite morphogenesis / negative regulation of phosphoprotein phosphatase activity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / glycogen metabolic process / molecular function inhibitor activity / ER overload response / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / protein kinase A catalytic subunit binding / NF-kappaB binding / canonical Wnt signaling pathway / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / hippocampus development / positive regulation of protein-containing complex assembly / positive regulation of cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / peptidyl-threonine phosphorylation / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / negative regulation of canonical Wnt signaling pathway / tau protein binding / Degradation of beta-catenin by the destruction complex / B-WICH complex positively regulates rRNA expression / regulation of circadian rhythm / beta-catenin binding / positive regulation of GTPase activity / circadian rhythm / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / cellular response to amyloid-beta / neuron projection development / Regulation of RUNX2 expression and activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / presynapse / insulin receptor signaling pathway / positive regulation of protein binding / kinase activity / postsynapse
Similarity search - Function
Glycogen synthase kinase-3 binding protein / Glycogen synthase kinase-3 binding / Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Glycogen synthase kinase-3 binding protein / Glycogen synthase kinase-3 binding / Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-B4K / Glycogen synthase kinase-3 beta / Proto-oncogene FRAT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBax, B.D. / Convery, M.A.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: From PIM1 to PI3K delta via GSK3 beta : Target Hopping through the Kinome.
Authors: Henley, Z.A. / Bax, B.D. / Inglesby, L.M. / Champigny, A. / Gaines, S. / Faulder, P. / Le, J. / Thomas, D.A. / Washio, Y. / Baldwin, I.R.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
X: Proto-oncogene FRAT1
Y: Proto-oncogene FRAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,97510
Polymers152,0224
Non-polymers9536
Water1086
1
A: Glycogen synthase kinase-3 beta
X: Proto-oncogene FRAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5846
Polymers76,0112
Non-polymers5724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-51 kcal/mol
Surface area17740 Å2
MethodPISA
2
B: Glycogen synthase kinase-3 beta
Y: Proto-oncogene FRAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3914
Polymers76,0112
Non-polymers3802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-32 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.686, 152.686, 212.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Glycogen synthase kinase-3 beta / / GSK-3 beta / Serine/threonine-protein kinase GSK3B


Mass: 46881.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Protein Proto-oncogene FRAT1 / Frequently rearranged in advanced T-cell lymphomas 1 / FRAT-1


Mass: 29129.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92837
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-B4K / ~{N}-[6-[3,4-bis(oxidanyl)phenyl]-1~{H}-pyrazolo[3,4-b]pyridin-3-yl]ethanamide


Mass: 284.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N4O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.6M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 15579 / % possible obs: 98.3 % / Redundancy: 7.14 % / Biso Wilson estimate: 100.18 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 26.3
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 7.14 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 808 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNG

1gng


Resolution: 3.2→19.97 Å / Cor.coef. Fo:Fc: 0.9461 / Cor.coef. Fo:Fc free: 0.9356 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.441
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 778 4.99 %RANDOM
Rwork0.194 ---
obs0.1957 15579 98.15 %-
Displacement parametersBiso mean: 96.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.1571 Å20 Å20 Å2
2--0.1571 Å20 Å2
3----0.3142 Å2
Refine analyzeLuzzati coordinate error obs: 0.697 Å
Refinement stepCycle: 1 / Resolution: 3.2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 62 6 5956
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016126HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.068357HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2031SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes129HARMONIC2
X-RAY DIFFRACTIONt_gen_planes887HARMONIC5
X-RAY DIFFRACTIONt_it6126HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion16.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion798SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6801SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2718 166 5.89 %
Rwork0.238 2652 -
all0.2401 2818 -
obs--98.15 %
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)
13.1880.84910.77292.0510.63763.7354-0.40060.2702-0.0039-0.28410.27420.23180.0825-0.2690.1264-0.029-0.1314-0.005-0.2875-0.024-0.2031103.610727.20712.3841
22.9007-0.4725-0.42222.16781.09532.9412-0.285-0.26910.0629-0.00860.2475-0.0312-0.2455-0.13630.03750.05860.2054-0.0115-0.26680.0187-0.1791105.872457.885634.2231
31.3474-2.0885-2.67654.18031.86312.46090.028-0.0191-0.0477-0.05860.0836-0.01480.10470.1198-0.11160.26510.18-0.1397-0.31510.01480.0452122.311510.638316.6335
4-0.56323.82080.17345.6967-0.78190.1578-0.0061-0.02540.0642-0.00490.0662-0.0087-0.08050.1333-0.060.3196-0.12310.1666-0.24020.07590.0321123.805472.924817.3543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ X|* }
4X-RAY DIFFRACTION4{ Y|* }

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