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- PDB-5itd: Crystal structure of PI3K alpha with PI3K delta inhibitor -

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Basic information

Entry
Database: PDB / ID: 5itd
TitleCrystal structure of PI3K alpha with PI3K delta inhibitor
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsTransferase/Protein Transport/Inhibitor / Inhibitor / lipid kinase / PI3K / alpha / delta / Transferase-Protein Transport-Inhibitor complex
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / negative regulation of actin filament depolymerization / phosphatidylinositol kinase activity / response to L-leucine / regulation of actin filament organization / response to butyrate / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / negative regulation of actin filament depolymerization / phosphatidylinositol kinase activity / response to L-leucine / regulation of actin filament organization / response to butyrate / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / interleukin-18-mediated signaling pathway / myeloid leukocyte migration / autosome genomic imprinting / phosphatidylinositol 3-kinase complex / T follicular helper cell differentiation / PI3K events in ERBB4 signaling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of cellular respiration / neurotrophin TRKA receptor binding / positive regulation of protein localization to membrane / Activated NTRK2 signals through PI3K / cis-Golgi network / negative regulation of fibroblast apoptotic process / Activated NTRK3 signals through PI3K / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / phosphatidylinositol 3-kinase complex, class IB / vasculature development / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / cardiac muscle cell contraction / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / kinase activator activity / Nephrin family interactions / anoikis / Signaling by LTK in cancer / phosphatidylinositol-3-phosphate biosynthetic process / positive regulation of leukocyte migration / Signaling by LTK / MET activates PI3K/AKT signaling / 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 / phosphatidylinositol 3-kinase / vascular endothelial growth factor signaling pathway / RND3 GTPase cycle / relaxation of cardiac muscle / insulin binding / growth hormone receptor signaling pathway / 1-phosphatidylinositol-3-kinase activity / Signaling by ALK / RHOV GTPase cycle / PI-3K cascade:FGFR3 / RHOB GTPase cycle / natural killer cell mediated cytotoxicity / negative regulation of macroautophagy / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / GP1b-IX-V activation signalling / PI-3K cascade:FGFR2 / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / negative regulation of osteoclast differentiation / response to dexamethasone / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / CDC42 GTPase cycle / negative regulation of anoikis / RET signaling / PI3K events in ERBB2 signaling / protein kinase activator activity / insulin receptor substrate binding / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / RHOG GTPase cycle / intercalated disc / regulation of multicellular organism growth / negative regulation of cell-matrix adhesion / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / positive regulation of TOR signaling / RAC2 GTPase cycle
Similarity search - Function
Ubiquitin-like (UB roll) - #770 / Helix Hairpins - #1490 / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 ...Ubiquitin-like (UB roll) - #770 / Helix Hairpins - #1490 / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / 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 / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / C2 domain / 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 / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Helix Hairpins / Alpha Horseshoe / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6CY / 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: 3.02 Å
AuthorsKnapp, M.S. / Elling, R.A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Discovery and Pharmacological Characterization of Novel Quinazoline-Based PI3K Delta-Selective Inhibitors.
Authors: Hoegenauer, K. / Soldermann, N. / Stauffer, F. / Furet, P. / Graveleau, N. / Smith, A.B. / Hebach, C. / Hollingworth, G.J. / Lewis, I. / Gutmann, S. / Rummel, G. / Knapp, M. / Wolf, R.M. / ...Authors: Hoegenauer, K. / Soldermann, N. / Stauffer, F. / Furet, P. / Graveleau, N. / Smith, A.B. / Hebach, C. / Hollingworth, G.J. / Lewis, I. / Gutmann, S. / Rummel, G. / Knapp, M. / Wolf, R.M. / Blanz, J. / Feifel, R. / Burkhart, C. / Zecri, F.
History
DepositionMar 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.0Apr 9, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / entity_poly / entity_src_gen / pdbx_contact_author / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_analyze / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _entity.pdbx_number_of_molecules ..._cell.volume / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_target_identifier / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_SU_R_free_Blow_DPI / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _reflns.B_iso_Wilson_estimate / _software.name / _software.version / _struct_sheet.number_strands / _symmetry.space_group_name_Hall
Provider: author / Type: Coordinate replacement

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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)164,5243
Polymers164,0312
Non-polymers4931
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-19 kcal/mol
Surface area52860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.645, 107.352, 134.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#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: 125287.828 Da / Num. of mol.: 1 / Mutation: M232K, L233K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Cell line (production host): Tn5 / Production host: unidentified baculovirus
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: 38743.484 Da / Num. of mol.: 1 / Fragment: UNP residues 2-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Cell (production host): Tn5 / Production host: unidentified baculovirus / References: UniProt: P27986
#3: Chemical ChemComp-6CY / 5-{4-[3-(4-acetylpiperazine-1-carbonyl)phenyl]quinazolin-6-yl}-2-methoxypyridine-3-carbonitrile


Mass: 492.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24N6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 3 uL of protein was mixed with 5 uL of well solution containing 12% PEG 3350 and 120 mM potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.82→48.76 Å / Num. obs: 36718 / % possible obs: 98.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 69.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 20.4 / Num. measured all: 268859 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.82-2.977.40.7963989853620.8070.3120.8562.6100
8.92-48.766.60.029868613070.9990.0120.03257.799.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house structure

Resolution: 3.02→48.76 Å / SU ML: 0.4023 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 1463 4.91 %RANDOM
Rwork0.2002 28359 --
obs0.2021 29822 98.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.26 Å2
Refinement stepCycle: LAST / Resolution: 3.02→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10004 0 37 20 10061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001910264
X-RAY DIFFRACTIONf_angle_d0.439613867
X-RAY DIFFRACTIONf_chiral_restr0.03821508
X-RAY DIFFRACTIONf_plane_restr0.00391781
X-RAY DIFFRACTIONf_dihedral_angle_d12.10643896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.130.36641450.30082854X-RAY DIFFRACTION100
3.13-3.250.31671480.262858X-RAY DIFFRACTION100
3.25-3.40.3211530.24572823X-RAY DIFFRACTION99.97
3.4-3.580.32021450.24342859X-RAY DIFFRACTION100
3.58-3.80.23791380.21032470X-RAY DIFFRACTION86.56
3.8-4.10.24081370.18712708X-RAY DIFFRACTION94.49
4.1-4.510.20631380.18412903X-RAY DIFFRACTION100
4.51-5.160.18851420.16222912X-RAY DIFFRACTION100
5.16-6.50.22261400.20232939X-RAY DIFFRACTION100
6.5-48.760.22091770.17723033X-RAY DIFFRACTION99.69
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)
15.5986078706-1.19389497137-1.110249731685.070624812620.6463791757064.60380658099-0.288537185307-0.1104801358920.142450407688-0.1322377447470.277937075607-0.1444474643370.1142051490430.5674044211190.003033008175570.509941502583-0.08750355417620.02307150752370.4669535373360.03105390102870.26300825911224.177947273534.6777486479-38.7478582466
22.03672909090.5342183764590.3171003107020.8342499542450.4847502522962.29813268365-0.0150496857356-0.1467538787890.522286215283-0.078155929563-0.007115914616540.285221428675-0.327471024123-0.107156694406-0.05742067539670.4990784424630.007864505078540.03226880405920.365699604472-0.02533726616640.63595408574-12.069782734434.490002043-28.4528599372
32.087221793260.5039234215020.08220454517031.316432787470.08463471209691.4551635943-0.06721299559230.05725248669510.29008663004-0.1286453896490.05458518396370.261712204809-0.2108838201-0.1236410261340.02624650137090.4000735772830.003647644616170.02835904181710.2912275676630.01229193306740.47626790286-12.054546590630.4914282975-31.3887548889
43.208157100680.4516051528090.3556505794461.64697254939-0.3524893040681.858947527720.122204615184-0.52802161079-0.3266891332590.126132943776-0.1307800909020.02484469521910.366275454442-0.231421331498-0.01970681107030.434045744462-0.06875815101510.03487821889720.4237839302330.05065622407040.479554811254-18.95161895759.76402015834-15.5986937456
50.614191153852-1.44878439376-0.09374697032753.44293982391.256007119292.25430892321-0.334236397730.419290094381-0.269206726212-0.03829750806930.0002906969676471.026656614840.550963162701-0.9553034601880.3559411134980.823899163538-0.341756330781-0.156235105261.17664668710.05950683129641.00639879757-44.695563892212.9999490763-44.9403121898
62.593704004383.46305354523-0.01520325933883.37882618422-0.100655243909-0.1190451342320.03304721426380.594550987129-0.2904157735790.1077702648430.261916097858-0.181925225899-0.0182171559606-0.0251670318887-0.1587570419820.788100241871-0.146612895671-0.06571873299890.6050678251030.01941002916620.6403048266612.0451618978515.8699422231-48.9829239637
77.567520548895.61957996058-0.9629552624164.41819472389-0.8704991981190.446477643021-0.3566150041230.776205737042-0.498182253648-0.3426404806470.459964365576-0.3694325985830.01988653359940.111479248883-0.03436152951950.661787220232-0.09725844648480.067199869330.691755923119-0.05663973469820.4756054079228.5247663438118.6700554029-52.9897934172
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 121 )AA2 - 1211 - 120
22chain 'A' and (resid 122 through 428 )AA122 - 428121 - 394
33chain 'A' and (resid 429 through 807 )AA429 - 807395 - 741
44chain 'A' and (resid 808 through 1052 )AA808 - 1052742 - 977
55chain 'B' and (resid 329 through 443 )BB329 - 4431 - 101
66chain 'B' and (resid 444 through 504 )BB444 - 504102 - 162
77chain 'B' and (resid 505 through 591 )BB505 - 591163 - 249

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