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- PDB-8v8v: PI3Ka H1047R co-crystal structure with inhibitor in cryptic pocke... -

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Basic information

Entry
Database: PDB / ID: 8v8v
TitlePI3Ka H1047R co-crystal structure with inhibitor in cryptic pocket near H1047R (compound 7).
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 / negative regulation of actin filament depolymerization / regulation of actin filament organization / 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 / negative regulation of actin filament depolymerization / regulation of actin filament organization / response to L-leucine / positive regulation of focal adhesion disassembly / response to butyrate / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / T follicular helper cell differentiation / autosome genomic imprinting / phosphatidylinositol 3-kinase complex / myeloid leukocyte migration / PI3K events in ERBB4 signaling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of cellular respiration / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / cis-Golgi network / ErbB-3 class receptor binding / negative regulation of fibroblast apoptotic process / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / 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 / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / kinase activator activity / anoikis / Signaling by LTK in cancer / phosphatidylinositol-3-phosphate biosynthetic process / positive regulation of leukocyte migration / relaxation of cardiac muscle / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / negative regulation of stress fiber assembly / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / RND1 GTPase cycle / positive regulation of filopodium assembly / phosphatidylinositol-4,5-bisphosphate 3-kinase / RND2 GTPase cycle / vascular endothelial growth factor signaling pathway / RND3 GTPase cycle / phosphatidylinositol 3-kinase / insulin binding / growth hormone receptor signaling pathway / 1-phosphatidylinositol-3-kinase activity / Signaling by ALK / RHOB GTPase cycle / RHOV GTPase cycle / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / GP1b-IX-V activation signalling / negative regulation of macroautophagy / natural killer cell mediated cytotoxicity / PI-3K cascade:FGFR2 / response to dexamethasone / 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 / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / CDC42 GTPase cycle / negative regulation of anoikis / RET signaling / PI3K events in ERBB2 signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / T cell differentiation / intercalated disc / protein kinase activator activity / RHOG GTPase cycle / extrinsic apoptotic signaling pathway via death domain receptors / regulation of multicellular organism growth / negative regulation of cell-matrix adhesion / RHOA GTPase cycle / CD28 dependent PI3K/Akt signaling / positive regulation of TOR signaling / Role of LAT2/NTAL/LAB on calcium mobilization
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: 2.61 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
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_symm_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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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)318,7678
Polymers317,0694
Non-polymers1,6984
Water1,982110
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)159,3834
Polymers158,5342
Non-polymers8492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-20 kcal/mol
Surface area50210 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)159,3834
Polymers158,5342
Non-polymers8492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-21 kcal/mol
Surface area54990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.172, 121.137, 163.902
Angle α, β, γ (deg.)90.00, 92.04, 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 / 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: 124867.469 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 (butterflies/moths)
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 / 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-YQ2 / 2-[[(1~{R})-1-(7-methyl-4-oxidanylidene-2-piperidin-1-yl-3~{H}-pyrido[1,2-a]pyrimidin-9-yl)ethyl]amino]benzoic acid


Mass: 407.485 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 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: Sep 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.61→73.77 Å / Num. obs: 79585 / % possible obs: 79.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 56.49 Å2 / Rpim(I) all: 0.093 / Net I/σ(I): 7.7
Reflection shellResolution: 2.61→2.7 Å / Num. unique obs: 5443 / Rpim(I) all: 0.45

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→73.77 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 41.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2879 1571 1.97 %
Rwork0.2372 --
obs0.2382 79571 79.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→73.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19904 0 120 112 20136
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.005 / Number: 3539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.690.52960.544843X-RAY DIFFRACTION54
2.69-2.790.55441030.50785212X-RAY DIFFRACTION59
2.79-2.90.47571180.4545611X-RAY DIFFRACTION63
2.9-3.030.50081160.40485993X-RAY DIFFRACTION68
3.03-3.190.38911310.35546611X-RAY DIFFRACTION74
3.19-3.390.38841410.29457140X-RAY DIFFRACTION80
3.39-3.660.31911520.24867808X-RAY DIFFRACTION88
3.66-4.020.27141730.21548318X-RAY DIFFRACTION93
4.02-4.610.23441730.17548620X-RAY DIFFRACTION97
4.61-5.80.21351830.18278817X-RAY DIFFRACTION99
5.8-73.770.23181850.18299027X-RAY DIFFRACTION99
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)
10.768-1.651.04843.5237-2.22971.40990.20910.87690.2917-0.9533-0.7768-0.2301-0.1255-0.94320.25561.75920.2141-0.09281.9978-0.00191.330636.7972-25.653-27.7533
20.98950.3821-2.11191.8395-0.24334.94670.43750.89660.7401-1.29930.3494-0.80340.0917-0.43770.23672.00070.08430.38261.17130.08731.56746.5359-25.0486-28.3121
32.97553.2929-0.7153.6809-0.50822.11960.53170.6586-0.1307-0.81450.8728-0.57850.0780.0834-0.63812.55030.06160.87251.29750.09381.578350.8178-34.2226-29.3069
40.87511.9294-0.56095.2686-1.10050.4498-0.47730.69371.52580.64580.2303-0.16330.0774-0.12890.29981.9123-0.0923-0.04851.30280.07641.538952.4927-31.4016-20.535
52.4821-1.3135-2.47610.89130.46686.5315-0.3899-0.0044-0.0914-0.4316-0.07420.0811-0.5739-1.3665-0.07151.78160.20170.04691.8368-0.08220.948733.2745-50.7317-17.596
60.62550.1994-0.69861.71271.35722.7823-0.2490.3156-0.20040.0381-0.06760.28780.22760.1440.06020.88260.17320.05010.6203-0.11980.521427.3075-24.741725.691
70.7528-0.1723-1.2041.65263.06926.4319-0.47290.2649-0.31490.2631-0.42030.4580.652-0.53380.41721.25420.12430.04060.6043-0.06770.518928.0525-29.399924.9247
82.34881.33311.70387.65060.16361.3308-0.05140.32870.5413-0.09660.22740.3159-0.0434-0.099-0.30451.3793-0.11380.03452.8665-0.03271.226416.0172-43.2204-16.7617
91.21010.00160.67661.25560.5951.71190.17510.2682-0.1102-0.1267-0.06120.0248-0.13660.4917-0.10120.904400.13220.3948-0.04330.428235.2224.866-88.4687
101.17420.76160.32961.85840.43860.9527-0.0473-0.1509-0.11670.09560.06740.166-0.0485-0.0619-0.05270.8833-0.04040.15090.3770.02540.445531.14610.1731-59.4217
111.57360.12570.77691.62070.68593.73740.1827-0.0493-0.15770.1677-0.08150.1625-0.1639-0.0088-0.04150.5261-0.06470.16350.21250.04830.396625.72628.5212-69.769
122.24640.03910.09410.7840.12442.44910.0629-0.43240.020.2982-0.12570.5433-0.295-0.4140.10770.67180.08070.19030.44820.0290.7061.964214.4838-65.6725
130.9261-0.0386-0.03651.26820.78322.9344-0.30620.46230.1496-0.0322-0.0213-0.0218-0.5286-0.06690.22111.1844-0.2541-0.02770.5567-0.04670.551940.923532.2014-88.0507
141.19731.19220.25841.19790.25980.05280.2067-0.6327-0.167-0.89370.1888-0.2074-0.7828-0.31730.15781.63170.07870.1122.8331-0.26711.7035.705545.1539-56.2552
151.2670.23020.7360.4607-0.06372.35170.08720.14260.19860.1410.02670.2366-0.2965-0.2811-0.09071.02920.1420.06050.50490.07580.401720.2718-3.840738.7817
161.1891-1.10380.12112.1354-0.32030.58890.06740.22770.191-0.2403-0.231-0.42320.09260.29280.09720.80750.07250.18970.57210.11530.540233.9967-1.43150.4714
172.2781-0.4771-0.87321.5696-0.31482.04310.08040.14370.2876-0.1397-0.1705-0.28520.15550.02720.11080.80130.10280.12480.40150.14970.472422.2496-3.20433.9001
183.59290.104-0.1481.0108-0.18591.73780.08261.2161-0.526-0.658-0.27260.0850.644-0.31250.09891.24960.08850.17970.96930.01820.46549.6594-13.9675-15.4009
194.26841.31822.36141.7612.5193.65290.5291.4237-1.52740.25-0.13780.5072-0.05710.11440.26221.7818-0.02150.23061.5925-0.2751.052139.2161-37.2353-28.1187
206.146-1.3125-2.88581.68821.74982.2656-0.7083-0.06530.61780.027-0.33550.1478-0.2432-0.48180.40921.26190.33220.10141.2914-0.35161.190740.3787-31.8329-12.4842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 355 through 367 )
2X-RAY DIFFRACTION2chain 'D' and (resid 368 through 400 )
3X-RAY DIFFRACTION3chain 'D' and (resid 401 through 410 )
4X-RAY DIFFRACTION4chain 'D' and (resid 411 through 430 )
5X-RAY DIFFRACTION5chain 'D' and (resid 431 through 441 )
6X-RAY DIFFRACTION6chain 'D' and (resid 442 through 514 )
7X-RAY DIFFRACTION7chain 'D' and (resid 515 through 587 )
8X-RAY DIFFRACTION8chain 'D' and (resid 588 through 600 )
9X-RAY DIFFRACTION9chain 'A' and (resid 2 through 198 )
10X-RAY DIFFRACTION10chain 'A' and (resid 199 through 553 )
11X-RAY DIFFRACTION11chain 'A' and (resid 554 through 784 )
12X-RAY DIFFRACTION12chain 'A' and (resid 785 through 1049 )
13X-RAY DIFFRACTION13chain 'B' and (resid 449 through 579 )
14X-RAY DIFFRACTION14chain 'B' and (resid 580 through 600 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 121 )
16X-RAY DIFFRACTION16chain 'C' and (resid 122 through 553 )
17X-RAY DIFFRACTION17chain 'C' and (resid 554 through 853 )
18X-RAY DIFFRACTION18chain 'C' and (resid 854 through 1047 )
19X-RAY DIFFRACTION19chain 'D' and (resid 326 through 340 )
20X-RAY DIFFRACTION20chain 'D' and (resid 341 through 354 )

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