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- PDB-9pe9: GSK3beta in complex with compound 6 -

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Basic information

Entry
Database: PDB / ID: 9pe9
TitleGSK3beta in complex with compound 6
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE/INHIBITOR / Kinase / cell cycle / cancer / TRANSFERASE / TRANSFERASE-INHIBITOR complex
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 / 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 ...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 / 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 cilium assembly / heart valve development / CRMPs in Sema3A signaling / tau-protein kinase / 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 / regulation of protein export from nucleus / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / 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 / cellular response to interleukin-3 / Maturation of nucleoprotein / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / regulation of microtubule-based process / AKT phosphorylates targets in the cytosol / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / Maturation of nucleoprotein / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / positive regulation of cell-matrix adhesion / regulation of axonogenesis / G protein-coupled dopamine receptor signaling pathway / glycogen metabolic process / ER overload response / regulation of dendrite morphogenesis / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / establishment of cell polarity / dynactin binding / epithelial to mesenchymal transition / Regulation of HSF1-mediated heat shock response / canonical Wnt signaling pathway / NF-kappaB binding / negative regulation of osteoblast differentiation / positive regulation of protein binding / 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 / cellular response to retinoic acid / extrinsic apoptotic signaling pathway in absence of ligand / 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 / negative regulation of cell migration / response to endoplasmic reticulum stress / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / excitatory postsynaptic potential / mitochondrion organization / Ubiquitin-dependent degradation of Cyclin D / hippocampus development / positive regulation of cell differentiation / positive regulation of protein-containing complex assembly / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / circadian rhythm / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / regulation of circadian rhythm / beta-catenin binding / peptidyl-serine phosphorylation / Degradation of beta-catenin by the destruction complex / B-WICH complex positively regulates rRNA expression / tau protein binding / Wnt signaling pathway / cellular response to amyloid-beta / neuron projection development / Regulation of RUNX2 expression and activity / positive regulation of protein catabolic process / kinase activity / p53 binding / insulin receptor signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of neuron apoptotic process
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / 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
Similarity search - Domain/homology
: / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsJohnson, E. / Chen, P.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of Atirmociclib (PF-07220060): A Potent and Selective CDK4 Inhibitor.
Authors: Gallego, G.M. / Palmer, C. / Orr, S. / Bernier, L. / Chen, P. / Cho-Schultz, S. / Deal, J.G. / Dress, K. / Edwards, M. / Jalaie, M. / Johnson, E. / Kania, R. / Kath, J.C. / Lafontaine, J. / ...Authors: Gallego, G.M. / Palmer, C. / Orr, S. / Bernier, L. / Chen, P. / Cho-Schultz, S. / Deal, J.G. / Dress, K. / Edwards, M. / Jalaie, M. / Johnson, E. / Kania, R. / Kath, J.C. / Lafontaine, J. / Ninkovic, S. / Sach, N. / Shen, H. / Anders, L. / Boras, B. / Cao, F. / Cianfrogna, J.A. / Cox, L. / Marroquin, L. / Pascual, B. / Petroski, M. / Quinlan, C. / Sacaan, A. / Wei, N. / Nair, S.K.
History
DepositionJul 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7334
Polymers81,7722
Non-polymers9612
Water6,720373
1
A: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3662
Polymers40,8861
Non-polymers4811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3662
Polymers40,8861
Non-polymers4811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.63, 109.25, 67.65
Angle α, β, γ (deg.)90, 100.99, 90
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40885.828 Da / Num. of mol.: 2 / Fragment: residues 29-385
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: Chemical ChemComp-A1CIF / (3R,4R)-4-({(4M)-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-1,3-benzimidazol-6-yl]pyrimidin-2-yl}amino)-1-(methanesulfonyl)piperidin-3-ol


Mass: 480.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26F2N6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop
Details: Well volume: 100.0 uL Well Ingredients: Buffer: 0.1 M (10.0 uL of stock 1.0 M) bicine (pH 9.00) Precipitant: 14.0 %w/v (35.0 uL of stock 40.0 %w/v) PEG 10000 Plate setup temperature: 21 C ...Details: Well volume: 100.0 uL Well Ingredients: Buffer: 0.1 M (10.0 uL of stock 1.0 M) bicine (pH 9.00) Precipitant: 14.0 %w/v (35.0 uL of stock 40.0 %w/v) PEG 10000 Plate setup temperature: 21 C Plate incubation temperature: 21 C Drop volume from well: 1.0 uL Drop protein volume: 1.0 uL Protein Formulation Composition: Protein: GSK3B (4.85 mg/mL) (0.12 mM) Compound: PF-6825089 (0.50 mM)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→21.21 Å / Num. obs: 54620 / % possible obs: 93.77 % / Redundancy: 3.4 % / CC1/2: 0.999 / Net I/σ(I): 14.92
Reflection shellResolution: 2.11→2.185 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.41 / Num. unique obs: 4170 / CC1/2: 0.839 / % possible all: 75.71

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
Aimlessdata scaling
autoBUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→21.21 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.211 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 2615 -RANDOM
Rwork0.22 ---
obs0.2214 52197 94.2 %-
Displacement parametersBiso mean: 43.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.4098 Å20 Å22.3083 Å2
2--0.5151 Å20 Å2
3----0.1053 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.11→21.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 66 373 5755
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085542HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.897556HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1888SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes958HARMONIC5
X-RAY DIFFRACTIONt_it5542HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion720SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4422SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion16.67
LS refinement shellResolution: 2.11→2.13 Å
RfactorNum. reflection% reflection
Rfree0.2773 50 -
Rwork0.2755 --
obs0.2756 1044 74.51 %
Refinement TLS params.

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)
10.3021-0.001-0.20360.15550.5851.86470.0701-0.00460.0647-0.0046-0.07520.07170.06470.07170.0051-0.05010.05670.0183-0.0150.02-0.001717.167914.30420.8076
20.9144-0.25240.07350-0.44050.4861-0.10110.00940.09830.00940.0341-0.17520.0983-0.17520.0670.0215-0.05880.03860.0425-0.0882-0.0584-5.3023-5.153519.2665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A36 - 382
2X-RAY DIFFRACTION1{ A|* }A900
3X-RAY DIFFRACTION2{ B|* }B36 - 382
4X-RAY DIFFRACTION2{ B|* }B900

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