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- PDB-3f7z: X-ray Co-Crystal Structure of Glycogen Synthase Kinase 3beta in C... -

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Basic information

Entry
Database: PDB / ID: 3f7z
TitleX-ray Co-Crystal Structure of Glycogen Synthase Kinase 3beta in Complex with an Inhibitor
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE / enzyme / protein kinase / inhibitor co-crystal structure / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Wnt signaling pathway
Function / homology
Function and homology information


neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling ...neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / 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 / negative regulation of protein acetylation / positive regulation of cilium assembly / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / regulation of microtubule-based process / regulation of protein export from nucleus / 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 long-term synaptic potentiation / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / Maturation of nucleoprotein / regulation of axon extension / negative regulation of epithelial to mesenchymal transition / G protein-coupled dopamine receptor signaling pathway / tau-protein kinase activity / positive regulation of cell-matrix adhesion / regulation of axonogenesis / regulation of dendrite morphogenesis / ER overload response / glycogen metabolic process / regulation of neuron projection development / establishment of cell polarity / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / negative regulation of osteoblast differentiation / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / NF-kappaB binding / canonical Wnt signaling pathway / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / positive regulation of autophagy / presynaptic modulation of chemical synaptic transmission / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of microtubule cytoskeleton organization / positive regulation of GTPase activity / negative regulation of cell migration / hippocampus development / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / excitatory postsynaptic potential / Ubiquitin-dependent degradation of Cyclin D / mitochondrion organization / positive regulation of cell differentiation / peptidyl-threonine phosphorylation / positive regulation of protein-containing complex assembly / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / regulation of circadian rhythm / beta-catenin binding / tau protein binding / Degradation of beta-catenin by the destruction complex / B-WICH complex positively regulates rRNA expression / circadian rhythm / cellular response to amyloid-beta / neuron projection development / positive regulation of protein catabolic process / Regulation of RUNX2 expression and activity / kinase activity / p53 binding / positive regulation of protein binding / positive regulation of neuron apoptotic process / insulin receptor signaling pathway
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-34O / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsMol, C.D. / Dougan, D.R.
CitationJournal: Bioorg.Med.Chem. / Year: 2009
Title: Design, synthesis and structure-activity relationships of 1,3,4-oxadiazole derivatives as novel inhibitors of glycogen synthase kinase-3beta.
Authors: Saitoh, M. / Kunitomo, J. / Kimura, E. / Hayase, Y. / Kobayashi, H. / Uchiyama, N. / Kawamoto, T. / Tanaka, T. / Mol, C.D. / Dougan, D.R. / Textor, G.S. / Snell, G.P. / Itoh, F.
History
DepositionNov 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4864
Polymers79,7662
Non-polymers7212
Water4,179232
1
A: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2432
Polymers39,8831
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2432
Polymers39,8831
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.622, 117.230, 67.351
Angle α, β, γ (deg.)90.000, 102.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycogen synthase kinase-3 beta / GSK-3 beta


Mass: 39882.773 Da / Num. of mol.: 2 / Fragment: UNP residues 35-383, Protein kinase domain
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
#2: Chemical ChemComp-34O / 2-(1,3-benzodioxol-5-yl)-5-[(3-fluoro-4-methoxybenzyl)sulfanyl]-1,3,4-oxadiazole


Mass: 360.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13FN2O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
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: 3.26 Å3/Da / Density % sol: 62.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 105 PEG 3350, 0.2M proline, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2006 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 37996 / % possible obs: 94.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.056 / Χ2: 1.029 / Net I/σ(I): 17.433
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.511 / Num. unique all: 3829 / Χ2: 0.971 / % possible all: 95.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
AMoREphasing
RefinementResolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.835 / SU B: 7.866 / SU ML: 0.186 / SU R Cruickshank DPI: 0.334 / SU Rfree: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1890 5 %RANDOM
Rwork0.203 ---
obs0.206 37843 94.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 90.68 Å2 / Biso mean: 30.561 Å2 / Biso min: 5.25 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-1.11 Å2
2--2.25 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5416 0 50 232 5698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225624
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9817659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6075674
X-RAY DIFFRACTIONr_chiral_restr0.0760.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024256
X-RAY DIFFRACTIONr_nbd_refined0.2010.22712
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.27
X-RAY DIFFRACTIONr_mcbond_it1.86123417
X-RAY DIFFRACTIONr_mcangle_it3.00535581
X-RAY DIFFRACTIONr_scbond_it2.0722207
X-RAY DIFFRACTIONr_scangle_it2.98132078
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.352 146
Rwork0.277 2637
all-2783
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)
12.74371.80761.38352.74560.46112.2074-0.07120.11920.2620.09580.0639-0.0635-0.10640.0520.00730.0707-0.0233-0.03160.11090.06690.23239.319315.787922.1417
21.30220.01010.05061.0269-0.62632.74980.0498-0.0185-0.0331-0.07830.0140.00020.355-0.3096-0.06380.1996-0.0789-0.00040.10180.03880.1162-7.3414-5.191815.5525
30.7341-0.42961.0514.7126-3.12174.8239-0.0223-0.13730.0711-0.18750.12150.03170.5526-0.1049-0.09920.2184-0.1382-0.03080.17380.05590.0201-24.31496.59448.9079
42.01670.8211-0.24190.8727-0.33991.69690.14770.0420.14110.0125-0.06450.1214-0.13530.0819-0.08320.1078-0.04310.01790.10350.02490.1876-26.792327.216431.0561
5-4.7579-19.701154.0337-8.55390.7964-1.7534-0.6515-0.66081.24190.88481.67260.41740.2788-0.2051-1.02110.0957-0.0792-0.11470.23040.14120.3407-0.494412.76617.8515
6-8.3222-17.93716.37822.849839.100714.2571-0.43470.42991.5441-0.66511.6814-0.85480.6621-0.3018-1.24670.4697-0.0477-0.1360.20420.01770.1026-26.15339.309138.3287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 136
2X-RAY DIFFRACTION2A137 - 383
3X-RAY DIFFRACTION3B35 - 136
4X-RAY DIFFRACTION4B137 - 383
5X-RAY DIFFRACTION5A3000
6X-RAY DIFFRACTION6B3000

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