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- PDB-8v8u: PI3Ka H1047R co-crystal structure with inhibitor in cryptic pocke... -

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Basic information

Entry
Database: PDB / ID: 8v8u
TitlePI3Ka H1047R co-crystal structure with inhibitor in cryptic pocket near H1047R (compound 12).
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsSIGNALING PROTEIN / H1047R / PI3K / PI3Ka
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 butyrate / phosphatidylinositol 3-kinase regulator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response ...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 butyrate / phosphatidylinositol 3-kinase regulator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / response to L-leucine / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / T follicular helper cell differentiation / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / phosphatidylinositol 3-kinase regulatory subunit binding / myeloid leukocyte migration / neurotrophin TRKA receptor binding / cellular response to hydrostatic pressure / positive regulation of focal adhesion disassembly / autosome genomic imprinting / Activated NTRK2 signals through PI3K / cis-Golgi network / negative regulation of fibroblast apoptotic process / TORC2 signaling / transmembrane receptor protein tyrosine kinase adaptor activity / Activated NTRK3 signals through PI3K / phosphatidylinositol 3-kinase complex, class IB / ErbB-3 class receptor binding / phosphatidylinositol 3-kinase complex / negative regulation of stress fiber assembly / positive regulation of protein localization to membrane / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / vasculature development / RHOD GTPase cycle / regulation of cellular respiration / Nephrin family interactions / anoikis / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by LTK in cancer / RHOF GTPase cycle / Signaling by LTK / kinase activator activity / positive regulation of leukocyte migration / relaxation of cardiac muscle / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / MET activates PI3K/AKT signaling / RND1 GTPase cycle / PI3K/AKT activation / phosphatidylinositol 3-kinase complex, class IA / RND2 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / RND3 GTPase cycle / positive regulation of filopodium assembly / cardiac muscle cell contraction / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / growth hormone receptor signaling pathway / insulin binding / Signaling by ALK / 1-phosphatidylinositol-3-kinase activity / RHOV GTPase cycle / vascular endothelial growth factor signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR3 / RHOB GTPase cycle / natural killer cell mediated cytotoxicity / GP1b-IX-V activation signalling / response to dexamethasone / negative regulation of macroautophagy / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / negative regulation of osteoclast differentiation / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / Synthesis of PIPs at the plasma membrane / intracellular glucose homeostasis / RHOU GTPase cycle / CDC42 GTPase cycle / RET signaling / negative regulation of anoikis / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / intercalated disc / PI3K Cascade / PI3K events in ERBB2 signaling / T cell differentiation / RHOG GTPase cycle / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of cell-matrix adhesion / CD28 dependent PI3K/Akt signaling / regulation of multicellular organism growth / Role of LAT2/NTAL/LAB on calcium mobilization / RHOA GTPase cycle / 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-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: 2.93 Å
AuthorsGunn, R.J. / Lawson, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of Pyridopyrimidinones that Selectively Inhibit the H1047R PI3K alpha Mutant Protein.
Authors: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / ...Authors: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / Gunn, R.J. / Ivetac, A. / Jones, B. / Kuehler, J. / Lawson, J.D. / Nguyen, N. / Parker, C. / Pearson, K.E. / Rahbaek, L. / Saechao, B. / Wang, X. / Waters, A. / Waters, L. / Watkins, A.H. / Olson, P. / Smith, C.R. / Christensen, J.G. / Marx, M.A.
History
DepositionDec 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,7018
Polymers316,9554
Non-polymers1,7464
Water19811
1
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)159,3504
Polymers158,4772
Non-polymers8732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-18 kcal/mol
Surface area60530 Å2
MethodPISA
2
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3504
Polymers158,4772
Non-polymers8732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-18 kcal/mol
Surface area57490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.633, 121.859, 163.881
Angle α, β, γ (deg.)90.00, 91.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform


Mass: 124810.422 Da / Num. of mol.: 2 / Mutation: H1047R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P42336
#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: 33666.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Production host: Trichoplusia ni (cabbage looper) / 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.: 2 / Source method: obtained synthetically / Formula: C19H22F3N5O2S / Comment: medication*YM
#4: Chemical ChemComp-YQB / (3S)-9-[(1R)-1-(2-carboxyanilino)ethyl]-3-cyano-7-methyl-4-oxo-2-(piperidin-1-yl)-3,4-dihydropyrido[1,2-a]pyrimidin-5-ium


Mass: 431.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.3-0.6 M Sodium Formate, 0.1 M Citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.93→84.6 Å / Num. obs: 64486 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rpim(I) all: 0.052 / Net I/σ(I): 10.8
Reflection shellResolution: 2.93→3.01 Å / Num. unique obs: 5227 / Rpim(I) all: 0.31

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Processing

Software
NameClassification
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→84.6 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 1791 2.78 %
Rwork0.2026 --
obs0.204 64368 90.04 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.93→84.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21902 0 0 11 21913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222384
X-RAY DIFFRACTIONf_angle_d0.56130204
X-RAY DIFFRACTIONf_dihedral_angle_d13.6218633
X-RAY DIFFRACTIONf_chiral_restr0.043236
X-RAY DIFFRACTIONf_plane_restr0.0043876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.010.4167980.39183820X-RAY DIFFRACTION72
3.01-3.10.41671100.37293954X-RAY DIFFRACTION74
3.1-3.20.43851360.34524199X-RAY DIFFRACTION79
3.2-3.310.37921220.30834446X-RAY DIFFRACTION83
3.31-3.450.37861240.28424676X-RAY DIFFRACTION88
3.45-3.60.31261340.24744837X-RAY DIFFRACTION91
3.6-3.790.28891550.21435029X-RAY DIFFRACTION94
3.79-4.030.26451450.19525135X-RAY DIFFRACTION96
4.03-4.340.22751480.1865222X-RAY DIFFRACTION98
4.34-4.780.19661520.15555237X-RAY DIFFRACTION98
4.78-5.470.20831540.16725320X-RAY DIFFRACTION99
5.47-6.890.2591580.19985324X-RAY DIFFRACTION99
6.89-84.60.20581550.16225378X-RAY DIFFRACTION98
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)
11.145-0.00370.36930.85070.48380.36340.09730.34-0.086-0.2370.0416-0.0336-0.40960.57040.01420.7571-0.13210.08090.6693-0.03890.472541.43310.2204-93.9016
20.46310.17770.50110.92430.87450.62080.0862-0.2298-0.08360.2859-0.07930.0590.0665-0.02520.0030.5965-0.178-0.00360.32450.03260.462826.58435.1204-65.0695
30.4083-0.0650.39280.38150.56050.8310.1249-0.0119-0.0890.2552-0.0877-0.1046-0.3489-0.15810.00041.0028-0.0437-0.01460.4680.00520.508837.058815.8716-41.1489
41.2776-0.09770.40730.62590.28760.65560.1125-0.1973-0.13020.1041-0.09150.2159-0.16790.01470.01250.3978-0.02130.01120.33240.03880.504812.753412.1906-67.1086
5-0.0518-0.0787-0.07360.06150.12830.02170.01430.1351-0.46330.60730.21760.28890.17770.001-0.00042.1542-0.11650.34452.155-0.06661.582421.329835.4018-32.7391
60.7258-0.56660.369-0.61220.48250.9666-0.4486-0.0325-0.066-0.2814-0.0944-0.1527-0.428-0.1671-0.3721.2432-0.1499-0.02930.7876-0.16560.640933.834136.6336-80.2953
70.2519-0.29870.72631.0452-1.00670.7124-0.11140.00190.27190.3272-0.0818-0.06920.1191-0.0792-0.01840.73380.0559-0.01850.56880.09140.558224.18350.001129.7346
8-0.2139-0.29170.10880.93210.20620.13790.03080.21990.1329-0.2724-0.1955-0.24880.12090.1678-0.0080.70430.19480.230.63370.29180.669937.1021-3.7252-3.7216
91.56410.35530.12350.4871-0.47410.6154-0.07370.24260.1737-0.1632-0.1799-0.13460.3445-0.0358-0.2490.77140.12070.110.50780.14630.45111.2941-8.9368-2.3846
10-0.013-0.0184-0.00750.019-0.03960.05070.03560.24870.3225-0.0841-0.38590.672-0.06480.05730.00011.35370.2717-0.04881.3323-0.0521.296839.5359-35.0677-25.0887
110.03620.03610.04230.00810.01420.013-0.225-0.4068-0.2567-0.3784-0.3482-0.03340.14270.05860.00281.81840.33170.0791.6304-0.07551.339242.0875-27.716-21.1743
120.0061-0.0039-0.01470.01380.01420.01610.05810.04490.1168-0.02450.2088-0.0728-0.00050.0793-0.00222.62630.40960.14991.43880.27961.675846.1584-24.2683-36.2768
130.1356-0.15040.01820.13550.0275-0.0375-0.10530.20170.24080.2116-0.3472-0.38270.1924-0.58620.00141.8470.16720.15151.31160.05411.512847.3646-35.9532-24.0412
140.67230.1313-0.56430.02950.63950.2589-0.1740.246-0.1808-0.06340.0861-0.0029-0.21870.2057-0.05021.06620.1068-0.03010.5742-0.11250.503727.6006-24.955225.7428
150.40080.06090.0354-0.07970.11040.0137-0.27690.2144-0.27650.5327-0.53760.39280.436-0.7428-0.31941.17520.08660.03750.6454-0.15620.541728.2885-29.246325.7708
160.06540.0139-0.03890.0682-0.00940.01870.1620.160.1149-0.12480.34540.0006-0.0359-0.15440.00241.27880.2-0.00391.9904-0.50081.477716.9258-43.3656-18.7662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 155 )
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 454 )
3X-RAY DIFFRACTION3chain 'A' and (resid 455 through 544 )
4X-RAY DIFFRACTION4chain 'A' and (resid 545 through 1055 )
5X-RAY DIFFRACTION5chain 'B' and (resid 322 through 432 )
6X-RAY DIFFRACTION6chain 'B' and (resid 433 through 600 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 178 )
8X-RAY DIFFRACTION8chain 'C' and (resid 179 through 647 )
9X-RAY DIFFRACTION9chain 'C' and (resid 648 through 1047 )
10X-RAY DIFFRACTION10chain 'D' and (resid 322 through 347 )
11X-RAY DIFFRACTION11chain 'D' and (resid 348 through 383 )
12X-RAY DIFFRACTION12chain 'D' and (resid 384 through 393 )
13X-RAY DIFFRACTION13chain 'D' and (resid 394 through 441 )
14X-RAY DIFFRACTION14chain 'D' and (resid 442 through 514 )
15X-RAY DIFFRACTION15chain 'D' and (resid 515 through 586 )
16X-RAY DIFFRACTION16chain 'D' and (resid 587 through 600 )

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