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- PDB-5hlp: X-RAY CRYSTAL STRUCTURE OF GSK3B IN COMPLEX WITH BRD3937 -

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Basic information

Entry
Database: PDB / ID: 5hlp
TitleX-RAY CRYSTAL STRUCTURE OF GSK3B IN COMPLEX WITH BRD3937
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase / 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 / beta-catenin destruction complex / CRMPs in Sema3A signaling / heart valve development / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / tau-protein kinase / regulation of microtubule-based process / 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 / 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 / regulation of axon extension / Maturation of nucleoprotein / tau-protein kinase activity / G protein-coupled dopamine receptor signaling pathway / negative regulation of epithelial to mesenchymal transition / positive regulation of cell-matrix adhesion / regulation of axonogenesis / regulation of dendrite morphogenesis / glycogen metabolic process / ER overload response / regulation of neuron projection development / establishment of cell polarity / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / epithelial to mesenchymal transition / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / 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 / 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 / response to endoplasmic reticulum stress / negative regulation of cell migration / positive regulation of protein export from nucleus / hippocampus development / positive regulation of protein ubiquitination / excitatory postsynaptic potential / Ubiquitin-dependent degradation of Cyclin D / mitochondrion organization / positive regulation of cell differentiation / positive regulation of protein-containing complex assembly / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / histone H3T45 kinase activity
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-65A / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsWhite, A. / Lakshminarasimhan, D. / Nadupalli, A. / Suto, R.K.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Inhibitors of Glycogen Synthase Kinase 3 with Exquisite Kinome-Wide Selectivity and Their Functional Effects.
Authors: Wagner, F.F. / Bishop, J.A. / Gale, J.P. / Shi, X. / Walk, M. / Ketterman, J. / Patnaik, D. / Barker, D. / Walpita, D. / Campbell, A.J. / Nguyen, S. / Lewis, M. / Ross, L. / Weiwer, M. / An, ...Authors: Wagner, F.F. / Bishop, J.A. / Gale, J.P. / Shi, X. / Walk, M. / Ketterman, J. / Patnaik, D. / Barker, D. / Walpita, D. / Campbell, A.J. / Nguyen, S. / Lewis, M. / Ross, L. / Weiwer, M. / An, W.F. / Germain, A.R. / Nag, P.P. / Metkar, S. / Kaya, T. / Dandapani, S. / Olson, D.E. / Barbe, A.L. / Lazzaro, F. / Sacher, J.R. / Cheah, J.H. / Fei, D. / Perez, J. / Munoz, B. / Palmer, M. / Stegmaier, K. / Schreiber, S.L. / Scolnick, E. / Zhang, Y.L. / Haggarty, S.J. / Holson, E.B. / Pan, J.Q.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)95,1904
Polymers94,5192
Non-polymers6712
Water1,874104
1
A: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5952
Polymers47,2591
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5952
Polymers47,2591
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.048, 67.667, 67.770
Angle α, β, γ (deg.)79.670, 76.660, 88.920
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 47259.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Plasmid: pAcG2T Baculogold / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-65A / 4-(2-methoxyphenyl)-3,7,7-trimethyl-1,6,7,8-tetrahydro-5H-pyrazolo[3,4-b]quinolin-5-one / BRD3937


Mass: 335.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% (W/V) PEG 5000 MME, 50 mM citric acid and 50 mM bis-tris propane, pH 5.0, 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.45→36.98 Å / Num. obs: 37928 / % possible obs: 92.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.097 / Χ2: 1.862 / Net I/av σ(I): 15.085 / Net I/σ(I): 10.5 / Num. measured all: 92123
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.45-2.542.50.63639801.21297.4
2.54-2.642.50.4539891.2597.5
2.64-2.762.50.33739931.43397.9
2.76-2.92.50.24340181.59397.8
2.9-3.092.50.16840271.89198.3
3.09-3.322.40.12640012.1998.3
3.32-3.662.40.10434362.49184
3.66-4.192.30.07327082.43266.2
4.19-5.282.30.06438852.35694.8
5.28-502.40.05638912.22395.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.45→36.98 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.506 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1912 5 %RANDOM
Rwork0.187 ---
obs0.1898 36014 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.96 Å2 / Biso mean: 54.142 Å2 / Biso min: 26.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.43 Å20.28 Å2
2--0.3 Å20.27 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 2.45→36.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5320 0 50 104 5474
Biso mean--42.47 49.96 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195525
X-RAY DIFFRACTIONr_bond_other_d0.0020.025247
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.9977559
X-RAY DIFFRACTIONr_angle_other_deg1.036312054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1785678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5123.203231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96715865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4121539
X-RAY DIFFRACTIONr_chiral_restr0.0970.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216168
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021251
X-RAY DIFFRACTIONr_mcbond_it4.3625.3182706
X-RAY DIFFRACTIONr_mcbond_other4.3595.3172705
X-RAY DIFFRACTIONr_mcangle_it6.4917.9623374
LS refinement shellResolution: 2.45→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 139 -
Rwork0.312 2586 -
all-2725 -
obs--88.62 %

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