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- PDB-7pg6: Crystal Structure of PI3Kalpha in complex with the inhibitor NVP-... -

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Basic information

Entry
Database: PDB / ID: 7pg6
TitleCrystal Structure of PI3Kalpha in complex with the inhibitor NVP-BYL719
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsTRANSFERASE / PI3K / PIK3CA / PIK3R1 / p110 / p85 / NVP-BYL719
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 / Phosphatidylinositol 3-kinase, accessory domain (PIK) ...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 / Phosphatidylinositol 3-kinase, accessory domain (PIK) / 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 / C2 domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-1LT / 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: 2.49943744477 Å
AuthorsGong, G. / Pinotsis, N. / Williams, R.L. / Vanhaesebroeck, B.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nature / Year: 2023
Title: A small-molecule PI3K alpha activator for cardioprotection and neuroregeneration.
Authors: Gong, G.Q. / Bilanges, B. / Allsop, B. / Masson, G.R. / Roberton, V. / Askwith, T. / Oxenford, S. / Madsen, R.R. / Conduit, S.E. / Bellini, D. / Fitzek, M. / Collier, M. / Najam, O. / He, Z. ...Authors: Gong, G.Q. / Bilanges, B. / Allsop, B. / Masson, G.R. / Roberton, V. / Askwith, T. / Oxenford, S. / Madsen, R.R. / Conduit, S.E. / Bellini, D. / Fitzek, M. / Collier, M. / Najam, O. / He, Z. / Wahab, B. / McLaughlin, S.H. / Chan, A.W.E. / Feierberg, I. / Madin, A. / Morelli, D. / Bhamra, A. / Vinciauskaite, V. / Anderson, K.E. / Surinova, S. / Pinotsis, N. / Lopez-Guadamillas, E. / Wilcox, M. / Hooper, A. / Patel, C. / Whitehead, M.A. / Bunney, T.D. / Stephens, L.R. / Hawkins, P.T. / Katan, M. / Yellon, D.M. / Davidson, S.M. / Smith, D.M. / Phillips, J.B. / Angell, R. / Williams, R.L. / Vanhaesebroeck, B.
History
DepositionAug 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)159,2784
Polymers158,8142
Non-polymers4642
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-24 kcal/mol
Surface area57940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.87, 105.19, 135.74
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 124458.984 Da / Num. of mol.: 1 / Mutation: M232K, L233K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Production host: Spodoptera frugiperda (fall armyworm)
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 / PI3-kinase regulatory subunit alpha / PI3K regulatory subunit alpha / PtdIns-3-kinase regulatory ...PI3-kinase regulatory subunit alpha / PI3K regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PI3-kinase subunit p85-alpha / PtdIns-3-kinase regulatory subunit p85-alpha


Mass: 34354.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27986
#3: Chemical ChemComp-1LT / (2S)-N~1~-{4-methyl-5-[2-(1,1,1-trifluoro-2-methylpropan-2-yl)pyridin-4-yl]-1,3-thiazol-2-yl}pyrrolidine-1,2-dicarboxamide / Alpelisib


Mass: 441.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22F3N5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 5000, 160 mM KSCN and 100 mM sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2019 / Details: KB-mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 52624 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 58.5772677043 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.217 / Net I/σ(I): 13.48
Reflection shellResolution: 2.499→2.65 Å / Redundancy: 13.7 % / Num. unique obs: 8343 / CC1/2: 0.469 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PG5

7pg5


Resolution: 2.49943744477→49.0422761719 Å / SU ML: 0.399134624379 / Cross valid method: FREE R-VALUE / σ(F): 1.33676695759 / Phase error: 28.413771157
RfactorNum. reflection% reflection
Rfree0.240324192397 2627 4.99809741248 %
Rwork0.187252392396 49933 -
obs0.189921800655 52560 99.7968367289 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 2.49943744477→49.0422761719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10585 0 31 59 10675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086023223474710901
X-RAY DIFFRACTIONf_angle_d1.2608516953214728
X-RAY DIFFRACTIONf_chiral_restr0.0479668767531592
X-RAY DIFFRACTIONf_plane_restr0.005806433555021898
X-RAY DIFFRACTIONf_dihedral_angle_d16.2995667224168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4995-2.54490.3803058046361300.3398605861582514X-RAY DIFFRACTION96.5668371074
2.5449-2.59380.3670723093661360.3179933572482575X-RAY DIFFRACTION100
2.5938-2.64680.3625898996731380.3090814044772631X-RAY DIFFRACTION99.9278238903
2.6468-2.70430.3659111097411360.3089586542562575X-RAY DIFFRACTION99.9631268437
2.7043-2.76720.3229649621661390.2860217181062637X-RAY DIFFRACTION99.9280057595
2.7672-2.83640.3758241992371360.2683324346632581X-RAY DIFFRACTION100
2.8364-2.91310.2924112346121390.2538229205732642X-RAY DIFFRACTION99.928135106
2.9131-2.99880.342176107831350.2351366570962566X-RAY DIFFRACTION100
2.9988-3.09560.3027719952331390.2355147200142640X-RAY DIFFRACTION100
3.0956-3.20620.322836253191350.2231481994682566X-RAY DIFFRACTION99.9629903775
3.2062-3.33450.2713053405381370.2038849109242606X-RAY DIFFRACTION100
3.3345-3.48630.2864190409031400.1977603560042648X-RAY DIFFRACTION100
3.4863-3.670.2436679125231380.187614867182631X-RAY DIFFRACTION100
3.67-3.89990.2116593053611390.1699631721772645X-RAY DIFFRACTION100
3.8999-4.20080.2109594736021390.1616908424912637X-RAY DIFFRACTION100
4.2008-4.62330.2078517790471390.1422646521792646X-RAY DIFFRACTION100
4.6233-5.29160.202474311861410.1413329711482677X-RAY DIFFRACTION100
5.2916-6.66420.1961752500491420.1786334688392690X-RAY DIFFRACTION100
6.6642-100.1725354911611490.1465986038282826X-RAY DIFFRACTION99.8322147651
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)
11.131678700880.2881056567880.1475230920010.5554027917170.03515499827150.615106046623-0.07281720386820.0374931441312-0.02124656848440.09601255445260.05715516412950.007225632486870.06871971755950.1823801946710.0406459590880.4913613122240.0520105267773-0.01063952799670.388419741358-0.01548276885920.42586877132817.9431532056-36.44076427138.1982047421
22.62325060585-0.24142610872-0.5660427565812.62796707578-1.873533327191.47997910297-0.1280385593031.04070372738-0.47393031939-0.675635946475-0.0475815016319-0.002293330619530.522507851-0.1928315542030.1356175532710.448781811011-0.04092858647320.01731239294990.540935200016-0.1608276050860.335020766552-4.66851366168-38.56497068871.74142096353
30.743513251589-0.103459572121-0.2002456280110.893079369556-0.2063318489130.997683657265-0.05694017368020.04300967066880.0154999118659-0.02937021156790.04329777190780.1478244886840.00336579722694-0.193923282701-0.003728006894630.352778880538-0.00844257973854-0.007914963963250.343123401851-0.02358484709130.36928351452-16.7989251509-22.091972312630.1610426462
40.458990431265-0.555718545309-0.00675459154830.933178055308-0.1664381658141.069542204220.0777177307837-0.09628789727160.07832440546990.2609507879840.02128402936640.925683569971-0.210905195246-0.491974121968-0.03622228892380.8296164948380.2421403505820.1416456284720.884961831832-0.06446673114840.98672221768-46.4727060259-13.605606481744.5003667762
51.1656838445-0.55066520463-0.154404263630.93847684431-0.005650697616320.760115923363-0.0605049583727-0.2051287572680.1364978827120.1607266010860.195593548373-0.0923424760328-0.01933966840690.0235470656806-0.1404530966280.618018520723-0.003591779342120.003597484413660.504089211176-0.02294840105770.5023760414864.93324988735-16.225622240351.5396917798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 3:160))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 161:313))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 323:1065))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 326:439))
5X-RAY DIFFRACTION5chain 'B' and ((resseq 440:591))

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