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- PDB-5xgh: Crystal structure of PI3K complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 5xgh
TitleCrystal structure of PI3K complex with an inhibitor
Components(Phosphatidylinositol ...) x 2
KeywordsTRANSFERASE/INHIBITOR / PI3K / inhibitor / TRANSFERASE-INHIBITOR complex
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 / phosphatidylinositol 3-kinase regulator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / regulation of actin filament organization / negative regulation of actin filament depolymerization / phosphatidylinositol 3-kinase activator activity ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / regulation of actin filament organization / negative regulation of actin filament depolymerization / phosphatidylinositol 3-kinase activator activity / response to butyrate / T follicular helper cell differentiation / IRS-mediated signalling / interleukin-18-mediated signaling pathway / phosphatidylinositol 3-kinase regulatory subunit binding / response to L-leucine / PI3K events in ERBB4 signaling / neurotrophin TRKA receptor binding / positive regulation of focal adhesion disassembly / cellular response to hydrostatic pressure / cis-Golgi network / Dengue Virus Attachment and Entry / Activated NTRK2 signals through PI3K / ErbB-3 class receptor binding / negative regulation of stress fiber assembly / transmembrane receptor protein tyrosine kinase adaptor activity / Activated NTRK3 signals through PI3K / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol 3-kinase complex / TORC2 signaling / Co-stimulation by ICOS / RHOD GTPase cycle / positive regulation of protein localization to membrane / Signaling by cytosolic FGFR1 fusion mutants / vasculature development / Nephrin family interactions / RHOF GTPase cycle / kinase activator activity / Signaling by LTK in cancer / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by LTK / anoikis / RND1 GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / positive regulation of filopodium assembly / RND2 GTPase cycle / MET activates PI3K/AKT signaling / PI3K/AKT activation / relaxation of cardiac muscle / RND3 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / growth hormone receptor signaling pathway / insulin binding / phosphatidylinositol 3-kinase / natural killer cell mediated cytotoxicity / phosphatidylinositol-3-phosphate biosynthetic process / Signaling by ALK / cardiac muscle cell contraction / RHOV GTPase cycle / 1-phosphatidylinositol-3-kinase activity / vascular endothelial growth factor signaling pathway / RHOB GTPase cycle / negative regulation of macroautophagy / GP1b-IX-V activation signalling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR3 / response to dexamethasone / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / positive regulation of protein kinase activity / PI-3K cascade:FGFR1 / RHOJ GTPase cycle / RHOC GTPase cycle / phosphatidylinositol phosphate biosynthetic process / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / phosphatidylinositol-mediated signaling / CDC42 GTPase cycle / RET signaling / negative regulation of anoikis / Interleukin-3, Interleukin-5 and GM-CSF signaling / T cell differentiation / PI3K events in ERBB2 signaling / RHOG GTPase cycle / insulin receptor substrate binding / intercalated disc / PI3K Cascade / Role of LAT2/NTAL/LAB on calcium mobilization / RAC3 GTPase cycle / RHOA GTPase cycle / CD28 dependent PI3K/Akt signaling / RAC2 GTPase cycle / Interleukin receptor SHC signaling / positive regulation of TOR signaling / Role of phospholipids in phagocytosis / enzyme-substrate adaptor activity / GAB1 signalosome / protein kinase activator activity / endothelial cell migration
Similarity search - Function
Helix Hairpins - #1490 / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3Kalpha, catalytic 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 ...Helix Hairpins - #1490 / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3Kalpha, catalytic 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 domain / SH2 domain / 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 / SHC Adaptor Protein / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Helix Hairpins / Alpha Horseshoe / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-84U / 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: 2.97 Å
AuthorsSong, K. / Yang, X. / Zhao, Y. / Jian, Z.
CitationJournal: Sci Rep / Year: 2017
Title: New Insights into PI3K Inhibitor Design using X-ray Structures of PI3K alpha Complexed with a Potent Lead Compound.
Authors: Yang, X. / Zhang, X. / Huang, M. / Song, K. / Li, X. / Huang, M. / Meng, L. / Zhang, J.
History
DepositionApr 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)156,2045
Polymers155,5792
Non-polymers6253
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-33 kcal/mol
Surface area55780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.360, 136.312, 149.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Phosphatidylinositol ... , 2 types, 2 molecules AB

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


Mass: 122083.289 Da / Num. of mol.: 1 / Fragment: UNP residues 8-1055
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-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: 33495.809 Da / Num. of mol.: 1 / Fragment: UNP residues 322-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27986

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Non-polymers , 4 types, 21 molecules

#3: Chemical ChemComp-84U / 3-[(4-fluorophenyl)methylamino]-5-(4-morpholin-4-ylthieno[3,2-d]pyrimidin-2-yl)phenol


Mass: 436.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21FN4O2S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.15M Lithium sulfate, 0.1M Tris-HCl pH 8.5, 28%(W/V) PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. obs: 30157 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 11.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2958 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.892 / SU B: 25.542 / SU ML: 0.452 / Cross valid method: THROUGHOUT / ESU R Free: 0.536
RfactorNum. reflection% reflectionSelection details
Rfree0.28012 1362 4.8 %RANDOM
Rwork0.2306 ---
obs0.23299 27298 94.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.005 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å2-0 Å2-0 Å2
2---3.72 Å20 Å2
3---2.13 Å2
Refinement stepCycle: 1 / Resolution: 2.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10480 0 42 18 10540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910745
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210328
X-RAY DIFFRACTIONr_angle_refined_deg0.9591.96614489
X-RAY DIFFRACTIONr_angle_other_deg0.817323786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.13851263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65324.325541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.396152031
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2471576
X-RAY DIFFRACTIONr_chiral_restr0.0530.21560
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022501
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2558.8225073
X-RAY DIFFRACTIONr_mcbond_other1.2548.8225072
X-RAY DIFFRACTIONr_mcangle_it2.30213.2246329
X-RAY DIFFRACTIONr_mcangle_other2.30213.2256330
X-RAY DIFFRACTIONr_scbond_it0.8078.9065672
X-RAY DIFFRACTIONr_scbond_other0.8078.9075668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.55313.3048155
X-RAY DIFFRACTIONr_long_range_B_refined4.15668.211885
X-RAY DIFFRACTIONr_long_range_B_other4.15668.211885
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 92 -
Rwork0.326 1716 -
obs--81.51 %

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