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- PDB-5dxu: p110delta/p85alpha with GDC-0326 -

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Basic information

Entry
Database: PDB / ID: 5dxu
Titlep110delta/p85alpha with GDC-0326
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
KeywordsTransferase/Inhibitor / lipid kinase / inhibitor / Transferase-Inhibitor complex
Function / homology
Function and homology information


B cell chemotaxis / Signaling by ALK / MET activates PI3K/AKT signaling / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle ...B cell chemotaxis / Signaling by ALK / MET activates PI3K/AKT signaling / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / RHOF GTPase cycle / FLT3 Signaling / RND3 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / PI3K events in ERBB4 signaling / Interleukin-7 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / IRS-mediated signalling / GPVI-mediated activation cascade / Signaling by SCF-KIT / Downstream signal transduction / PI3K/AKT activation / Role of phospholipids in phagocytosis / Tie2 Signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / PI3K Cascade / PIP3 activates AKT signaling / GP1b-IX-V activation signalling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Synthesis of PIPs at the plasma membrane / RHOA GTPase cycle / DAP12 signaling / RHOU GTPase cycle / RHOV GTPase cycle / mast cell differentiation / mast cell chemotaxis / Regulation of signaling by CBL / Downstream TCR signaling / natural killer cell differentiation / RHOG GTPase cycle / positive regulation of epithelial tube formation / RET signaling / natural killer cell chemotaxis / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / neutrophil extravasation / positive regulation of neutrophil apoptotic process / phosphatidylinositol 3-kinase regulator activity / respiratory burst involved in defense response / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / T cell chemotaxis / natural killer cell activation / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / Extra-nuclear estrogen signaling / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / vascular endothelial growth factor signaling pathway / G alpha (q) signalling events / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / mast cell degranulation / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / B cell activation / intracellular glucose homeostasis / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / Synthesis of PIPs at the plasma membrane / T cell differentiation / RET signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / phosphatidylinositol 3-kinase binding / positive regulation of endothelial cell proliferation / insulin-like growth factor receptor binding / T cell activation / response to endoplasmic reticulum stress / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / B cell differentiation
Similarity search - Function
Ubiquitin-like (UB roll) - #770 / PI3Kdelta, 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-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) ...Ubiquitin-like (UB roll) - #770 / PI3Kdelta, 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-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / 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 / C2 domain / 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. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Rho GTPase activation protein / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / Ubiquitin-like (UB roll) / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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-5H5 / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform / Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsHeffron, T.P. / Heald, R.A. / Ndubaku, C. / Wei, B.Q. / Augustin, M. / Do, S. / Edgar, K. / Eigenbrot, C. / Friedman, L. / Gancia, E. ...Heffron, T.P. / Heald, R.A. / Ndubaku, C. / Wei, B.Q. / Augustin, M. / Do, S. / Edgar, K. / Eigenbrot, C. / Friedman, L. / Gancia, E. / Jackson, P.S. / Jones, G. / Kolesnikov, A. / Lee, L.B. / Lesnick, J.D. / Lewis, C. / McLean, N. / Mortle, M. / Nonomiya, J. / Pang, J. / Price, S. / Prior, W.W. / Salphati, L. / Sideris, S. / Staben, S.T. / Steinbacher, S. / Tsui, V. / Wallin, J. / Sampath, D. / Olivero, A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: The Rational Design of Selective Benzoxazepin Inhibitors of the alpha-Isoform of Phosphoinositide 3-Kinase Culminating in the Identification of (S)-2-((2-(1-Isopropyl-1H-1,2,4-triazol-5-yl)- ...Title: The Rational Design of Selective Benzoxazepin Inhibitors of the alpha-Isoform of Phosphoinositide 3-Kinase Culminating in the Identification of (S)-2-((2-(1-Isopropyl-1H-1,2,4-triazol-5-yl)-5,6-dihydrobenzo[f]imidazo[1,2-d][1,4]oxazepin-9-yl)oxy)propanamide (GDC-0326).
Authors: Heffron, T.P. / Heald, R.A. / Ndubaku, C. / Wei, B. / Augistin, M. / Do, S. / Edgar, K. / Eigenbrot, C. / Friedman, L. / Gancia, E. / Jackson, P.S. / Jones, G. / Kolesnikov, A. / Lee, L.B. / ...Authors: Heffron, T.P. / Heald, R.A. / Ndubaku, C. / Wei, B. / Augistin, M. / Do, S. / Edgar, K. / Eigenbrot, C. / Friedman, L. / Gancia, E. / Jackson, P.S. / Jones, G. / Kolesnikov, A. / Lee, L.B. / Lesnick, J.D. / Lewis, C. / McLean, N. / Mortl, M. / Nonomiya, J. / Pang, J. / Price, S. / Prior, W.W. / Salphati, L. / Sideris, S. / Staben, S.T. / Steinbacher, S. / Tsui, V. / Wallin, J. / Sampath, D. / Olivero, A.G.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,7643
Polymers140,3812
Non-polymers3821
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-17 kcal/mol
Surface area52530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.049, 108.749, 142.427
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 delta isoform / PtdIns-3-kinase subunit delta / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic ...PtdIns-3-kinase subunit delta / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit delta / p110delta


Mass: 119501.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CD / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O00329, phosphatidylinositol-4,5-bisphosphate 3-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: 20879.555 Da / Num. of mol.: 1 / Fragment: UNP residues 431-599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PIK3R1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23727
#3: Chemical ChemComp-5H5 / (2S)-2-({2-[1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl}oxy)propanamide / GDC-0326


Mass: 382.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.6 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.64→86.43 Å / Num. obs: 40514 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.046 / Net I/σ(I): 13.8
Reflection shellResolution: 2.64→2.73 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.8 / % possible all: 97.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→86.43 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.907 / SU B: 33.168 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R: 0.872 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28419 836 2.1 %RANDOM
Rwork0.24783 ---
obs0.24858 39678 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 83.578 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å20 Å20 Å2
2--3.9 Å20 Å2
3----7.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.358 Å0.872 Å
Refinement stepCycle: LAST / Resolution: 2.64→86.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8923 0 28 4 8955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228823
X-RAY DIFFRACTIONr_bond_other_d0.0020.028011
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.96611950
X-RAY DIFFRACTIONr_angle_other_deg0.868318520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45851080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10224.199412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.483151517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3061556
X-RAY DIFFRACTIONr_chiral_restr0.0590.21337
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021780
X-RAY DIFFRACTIONr_nbd_refined0.1650.21713
X-RAY DIFFRACTIONr_nbd_other0.1240.27478
X-RAY DIFFRACTIONr_nbtor_refined0.1550.24203
X-RAY DIFFRACTIONr_nbtor_other0.0750.24711
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0780.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1430.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.22627104
X-RAY DIFFRACTIONr_mcbond_other0.19922189
X-RAY DIFFRACTIONr_mcangle_it1.53238733
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.38643948
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.50563217
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.64→2.709 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 56 -
Rwork0.317 2919 -
obs--96.97 %
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)
13.65421.0929-2.87753.2254-1.05286.0878-0.176-0.00060.10570.11010.1661-0.1255-0.03960.0130.0098-0.181-0.06550.0117-0.1358-0.0051-0.096643.39717.293-11.39
21.60510.1557-0.54124.09352.18244.64790.1878-0.13990.58560.09990.1679-0.2158-1.07080.1229-0.35570.1981-0.00980.0692-0.0390.050.194522.72834.42617.298
31.7728-0.1085-0.55813.42140.41612.0274-0.22070.2244-0.3989-0.1596-0.01960.55780.5839-0.33790.24020.2312-0.17210.03310.0689-0.11180.12296.155-8.7957.22
44.0701-0.1504-1.21521.72840.36541.7721-0.11580.266-0.34550.07660.06330.6020.2381-0.63430.0525-0.1265-0.0381-0.0244-0.05290.0670.0657-0.22510.75817.357
53.00850.2854-1.65631.4846-0.03114.3939-0.0092-0.2157-0.0540.1417-0.0267-0.4047-0.19660.86950.0359-0.1026-0.0386-0.0702-0.0390.0581-0.003535.54116.5622.95
62.65330.85821.11920.99240.1365.24970.1056-0.2868-0.17940.429-0.124-0.12490.01210.22850.01840.0948-0.0241-0.0495-0.11340.03640.014621.92912.55145.178
72.18591.6039-3.78021.5886-3.53659.0987-0.1806-0.1076-0.2283-0.1452-0.1288-0.20410.24480.32060.30950.0857-0.04050.0822-0.1111-0.06090.085729.289-9.1918.185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 108
2X-RAY DIFFRACTION2A109 - 278
3X-RAY DIFFRACTION3A279 - 474
4X-RAY DIFFRACTION4A475 - 675
5X-RAY DIFFRACTION5A676 - 830
6X-RAY DIFFRACTION6A831 - 1031
7X-RAY DIFFRACTION7B431 - 599

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