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- PDB-8sbc: Co-structure of Phosphatidylinositol 4,5-bisphosphate 3-kinase ca... -

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Basic information

Entry
Database: PDB / ID: 8sbc
TitleCo-structure of Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform and brain penetrant inhibitors
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsTRANSFERASE / lipid kinase / mutant / p85 / niSH2 / brain-penetrant / mTOR
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / phosphatidylinositol kinase activity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to L-leucine / positive regulation of focal adhesion disassembly / response to butyrate / 1-phosphatidylinositol-3-kinase regulator activity ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / phosphatidylinositol kinase activity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to L-leucine / positive regulation of focal adhesion disassembly / response to butyrate / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / T follicular helper cell differentiation / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase regulatory subunit binding / autosome genomic imprinting / myeloid leukocyte migration / regulation of cellular respiration / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / cis-Golgi network / negative regulation of fibroblast apoptotic process / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / ErbB-3 class receptor binding / phosphatidylinositol 3-kinase complex, class IB / positive regulation of protein localization to membrane / vasculature development / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / RHOD GTPase cycle / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IA / RHOF GTPase cycle / Nephrin family interactions / kinase activator activity / Signaling by LTK in cancer / anoikis / phosphatidylinositol-3-phosphate biosynthetic process / positive regulation of leukocyte migration / Signaling by LTK / MET activates PI3K/AKT signaling / relaxation of cardiac muscle / PI3K/AKT activation / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / negative regulation of stress fiber assembly / RND1 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / positive regulation of filopodium assembly / RND2 GTPase cycle / RND3 GTPase cycle / vascular endothelial growth factor signaling pathway / phosphatidylinositol 3-kinase / growth hormone receptor signaling pathway / insulin binding / 1-phosphatidylinositol-3-kinase activity / Signaling by ALK / PI-3K cascade:FGFR3 / RHOV GTPase cycle / RHOB GTPase cycle / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / natural killer cell mediated cytotoxicity / GP1b-IX-V activation signalling / negative regulation of macroautophagy / PI-3K cascade:FGFR2 / response to dexamethasone / PI-3K cascade:FGFR4 / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / phosphatidylinositol phosphate biosynthetic process / intracellular glucose homeostasis / negative regulation of osteoclast differentiation / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / RET signaling / CDC42 GTPase cycle / negative regulation of anoikis / PI3K events in ERBB2 signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / insulin receptor substrate binding / intercalated disc / T cell differentiation / RHOG GTPase cycle / negative regulation of cell-matrix adhesion / extrinsic apoptotic signaling pathway via death domain receptors / regulation of multicellular organism growth / protein kinase activator activity / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC2 GTPase cycle
Similarity search - Function
PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain ...PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Rho GTPase activation protein / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-ZTV / Phosphatidylinositol 3-kinase regulatory subunit alpha / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKnapp, M.S. / Elling, R.A. / Tang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Identification of Brain-Penetrant ATP-Competitive mTOR Inhibitors for CNS Syndromes.
Authors: Bonazzi, S. / Gray, A. / Thomsen, N.M. / Biag, J. / Labbe-Giguere, N. / Keaney, E.P. / Malik, H.A. / Sun, Y. / Nunez, J. / Karki, R.G. / Knapp, M. / Elling, R. / Fuller, J. / Pardee, G. / ...Authors: Bonazzi, S. / Gray, A. / Thomsen, N.M. / Biag, J. / Labbe-Giguere, N. / Keaney, E.P. / Malik, H.A. / Sun, Y. / Nunez, J. / Karki, R.G. / Knapp, M. / Elling, R. / Fuller, J. / Pardee, G. / Craig, L. / Capre, K. / Salas, S. / Gorde, A. / Liang, G. / Lubicka, D. / McTighe, S.M. / Goold, C. / Liu, S. / Deng, L. / Hong, J. / Fekete, A. / Stadelmann, P. / Frieauff, W. / Elhajouji, A. / Bauer, D. / Lerchner, A. / Radetich, B. / Furet, P. / Piizzi, G. / Burdette, D. / Wilson, C.J. / Peukert, S. / Hamann, L.G. / Murphy, L.O. / Curtis, D.
History
DepositionApr 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,9214
Polymers160,4312
Non-polymers4912
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-40 kcal/mol
Surface area51250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.077, 107.847, 133.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / PI3-kinase subunit alpha / PI3K-alpha / PI3Kalpha / PtdIns-3-kinase subunit alpha / ...PI3-kinase subunit alpha / PI3K-alpha / PI3Kalpha / PtdIns-3-kinase subunit alpha / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha / PtdIns-3-kinase subunit p110-alpha / p110alpha / Phosphoinositide 3-kinase alpha / Phosphoinositide-3-kinase catalytic alpha polypeptide / Serine/threonine protein kinase PIK3CA


Mass: 125287.875 Da / Num. of mol.: 1 / Mutation: M232K, L233K, W780K, I800M, V850W, F930V
Source method: isolated from a genetically manipulated source
Details: Multiple mutations to alter ligand binding characteristics of the ATP binding site M232K, L233K, W780K, I800M, V850W, F930V
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Cell line (production host): Sf21 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: P42336, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PtdIns-3-kinase regulatory subunit p85-alpha


Mass: 35142.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The difference at 306 is due to remains of cleavage site
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Cell line (production host): Sf21 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P27986
#3: Chemical ChemComp-ZTV / (2M)-7-[(3R)-3-methylmorpholin-4-yl]-5-[(3S)-3-methylmorpholin-4-yl]-2-(pyridin-2-yl)-1H-imidazo[4,5-b]pyridine


Mass: 394.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: RESERVOIR SOLUTION : 12%-20% PEG 3350, 0.125M-0.20M KSCN PROTEIN SOLUTION : 20MM TRIS PH 7.2, 200MM NACL, 1% BETAINE, 1% ETHYLENE GLYCOL, 0.02% CHAPS, 5MM DTT, PROTEIN IS 7.4 MG/ML FORMATION ...Details: RESERVOIR SOLUTION : 12%-20% PEG 3350, 0.125M-0.20M KSCN PROTEIN SOLUTION : 20MM TRIS PH 7.2, 200MM NACL, 1% BETAINE, 1% ETHYLENE GLYCOL, 0.02% CHAPS, 5MM DTT, PROTEIN IS 7.4 MG/ML FORMATION METHOD : SOAKING PROTOCOL : SET UP APO XTALS DROPS IN 1:1 RATIO IN 30C, REMARK 280 XTALS GROW OVERNIGHT, THEN ADD 2MM OF STOCK CPD AND INCUBATE FOR A FEW HOURS METHOD : VAPOR DIFFUSION - HANGING DROP TEMPERATURE : 303.0 CRYO PROTOCOL : 20% ETHYLENE GLYCOL PLUS WELL SOLUTION

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→83.95 Å / Num. obs: 64894 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.023 / Rrim(I) all: 0.079 / Χ2: 0.76 / Net I/σ(I): 15.9 / Num. measured all: 823656
Reflection shellResolution: 2.3→2.42 Å / % possible obs: 99 % / Redundancy: 12 % / Rmerge(I) obs: 1.522 / Num. measured all: 111247 / Num. unique obs: 9289 / CC1/2: 0.844 / Rpim(I) all: 0.454 / Rrim(I) all: 1.59 / Χ2: 0.53 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→83.95 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 3181 4.93 %Random
Rwork0.2407 ---
obs0.2423 64537 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→83.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9658 0 34 34 9726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029934
X-RAY DIFFRACTIONf_angle_d0.38613493
X-RAY DIFFRACTIONf_dihedral_angle_d11.6013623
X-RAY DIFFRACTIONf_chiral_restr0.0371498
X-RAY DIFFRACTIONf_plane_restr0.0031744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.47321290.46352419X-RAY DIFFRACTION90
2.33-2.370.48661330.41412639X-RAY DIFFRACTION100
2.37-2.410.45091470.40342612X-RAY DIFFRACTION100
2.41-2.450.44741370.37882687X-RAY DIFFRACTION100
2.45-2.50.35791240.35632614X-RAY DIFFRACTION99
2.5-2.540.44041150.33142676X-RAY DIFFRACTION100
2.54-2.60.32251260.31292627X-RAY DIFFRACTION100
2.6-2.650.30781390.30442681X-RAY DIFFRACTION100
2.65-2.710.33511430.29042620X-RAY DIFFRACTION100
2.71-2.780.35591170.30382708X-RAY DIFFRACTION100
2.78-2.860.31621520.28922618X-RAY DIFFRACTION100
2.86-2.940.30811260.31112674X-RAY DIFFRACTION100
2.94-3.040.35971180.32712692X-RAY DIFFRACTION100
3.04-3.140.39171490.33162650X-RAY DIFFRACTION100
3.15-3.270.31591560.29562659X-RAY DIFFRACTION100
3.27-3.420.34171480.26422658X-RAY DIFFRACTION100
3.42-3.60.29271610.2482663X-RAY DIFFRACTION100
3.6-3.830.28491320.24692703X-RAY DIFFRACTION100
3.83-4.120.24971470.22112690X-RAY DIFFRACTION100
4.12-4.540.22481080.19692743X-RAY DIFFRACTION100
4.54-5.190.22091350.18732733X-RAY DIFFRACTION100
5.19-6.540.23571550.22062735X-RAY DIFFRACTION100
6.54-83.950.20881840.18272855X-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)
12.8503-1.2918-1.20111.0103-0.12381.71740.23760.65710.9859-0.2586-0.1611-0.48950.0246-0.0819-0.06520.49390.04580.1180.54140.0930.835894.5356145.088426.3933
24.6554-1.470.07981.6481-0.16441.7364-0.0873-0.36361.24880.0350.0299-0.6925-0.2170.19790.04640.3808-0.00890.0250.4087-0.13280.9165115.21137.195838.6357
34.7515-2.2998-0.62993.05591.45042.26140.53070.84310.0562-0.4378-0.4414-0.3510.12720.0401-0.08520.58980.08180.17760.56680.00520.5356117.2558118.396516.76
47.2722-2.2373-2.21712.61121.23355.2047-0.6675-0.534-0.6536-0.0551-0.1746-0.43910.35360.27980.79170.54790.0450.13550.92780.12931.5281145.2206122.343843.2594
54.5394-0.7359-0.48050.4037-0.69294.00360.2856-1.9599-0.54310.2293-0.6549-1.5969-0.38550.4350.27450.69180.06510.01231.25060.14451.4385148.1376123.858351.7923
66.5808-6.2806-1.56295.86871.67521.058-0.1938-0.9403-0.50980.15290.42230.31570.0910.1156-0.19770.48590.05320.01530.58270.03090.608595.5898123.722850.8285
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 341 )
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 784 )
3X-RAY DIFFRACTION3chain 'A' and (resid 785 through 1053 )
4X-RAY DIFFRACTION4chain 'B' and (resid 326 through 400 )
5X-RAY DIFFRACTION5chain 'B' and (resid 401 through 435 )
6X-RAY DIFFRACTION6chain 'B' and (resid 436 through 591 )

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