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- PDB-8gk5: EGFR(T790M/V948R) kinase in complex with osimertinib and benzimid... -

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Open data


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Basic information

Entry
Database: PDB / ID: 8gk5
TitleEGFR(T790M/V948R) kinase in complex with osimertinib and benzimidazole allosteric inhibitor
ComponentsEpidermal growth factor receptor
KeywordsTRANSFERASE/INHIBITOR / EGFR / kinase / covalent / inhibitor / allosteric / cancer / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A ...multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / Signaling by EGFR / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hair follicle development / MAP kinase kinase kinase activity / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / salivary gland morphogenesis / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / ossification / SHC1 events in ERBB2 signaling / basal plasma membrane / positive regulation of DNA repair / cellular response to epidermal growth factor stimulus / positive regulation of DNA replication / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / cell-cell adhesion / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / negative regulation of protein catabolic process / Signaling by ERBB2 KD Mutants / positive regulation of miRNA transcription / kinase binding / ruffle membrane / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / positive regulation of protein phosphorylation / cell morphogenesis / positive regulation of fibroblast proliferation / neuron differentiation / HCMV Early Events / Constitutive Signaling by Aberrant PI3K in Cancer / actin filament binding / cell junction / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / virus receptor activity / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / double-stranded DNA binding / protein tyrosine kinase activity / early endosome membrane / protein phosphatase binding / nuclear membrane / basolateral plasma membrane / learning or memory / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-Q6K / : / Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBeyett, T.S. / Eck, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA116020-16 United States
CitationJournal: To be published
Title: Development of benzimidazole allosteric EGFR kinase inhibitors
Authors: Beyett, T.S. / Eck, M.J.
History
DepositionMar 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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: Epidermal growth factor receptor
B: Epidermal growth factor receptor
C: Epidermal growth factor receptor
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,02712
Polymers150,8984
Non-polymers4,1298
Water2,378132
1
A: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7573
Polymers37,7251
Non-polymers1,0322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7573
Polymers37,7251
Non-polymers1,0322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7573
Polymers37,7251
Non-polymers1,0322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7573
Polymers37,7251
Non-polymers1,0322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.569, 73.057, 119.105
Angle α, β, γ (deg.)90.00, 118.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 37724.598 Da / Num. of mol.: 4 / Fragment: kinase domain / Mutation: T790M, V948R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-Q6K / ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide


Mass: 501.623 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H35N7O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-YW5 / 2-[(R)-(1H-benzimidazol-2-yl)(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-2,3-dihydro-1H-isoindol-1-one


Mass: 530.635 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H31FN4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 0.1 M Bis-Tris pH 5.7, 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→65.63 Å / Num. obs: 101280 / % possible obs: 96.5 % / Redundancy: 2.9 % / CC1/2: 0.989 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.077 / Rrim(I) all: 0.135 / Net I/σ(I): 8.2
Reflection shellResolution: 2.3→2.34 Å / % possible obs: 96.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.76 / Num. measured all: 7846 / Num. unique obs: 2725 / CC1/2: 0.199 / Rpim(I) all: 0.549 / Rrim(I) all: 0.943 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
DIALSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→65.63 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 5183 5.12 %
Rwork0.2224 --
obs0.2239 101280 90.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→65.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9465 0 308 132 9905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510035
X-RAY DIFFRACTIONf_angle_d0.7613600
X-RAY DIFFRACTIONf_dihedral_angle_d15.9823786
X-RAY DIFFRACTIONf_chiral_restr0.0521470
X-RAY DIFFRACTIONf_plane_restr0.0051688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.34392010.3263171X-RAY DIFFRACTION89
2.33-2.360.36361890.31443166X-RAY DIFFRACTION92
2.36-2.380.3341980.3093207X-RAY DIFFRACTION91
2.38-2.410.30831710.31023251X-RAY DIFFRACTION92
2.41-2.450.32051760.29483265X-RAY DIFFRACTION91
2.45-2.480.31881560.28273151X-RAY DIFFRACTION91
2.48-2.520.31731740.29863173X-RAY DIFFRACTION89
2.52-2.550.291370.27892989X-RAY DIFFRACTION86
2.55-2.590.30971790.27133198X-RAY DIFFRACTION89
2.59-2.640.29611950.26193234X-RAY DIFFRACTION93
2.64-2.680.30141720.26693261X-RAY DIFFRACTION93
2.68-2.730.27531670.26693336X-RAY DIFFRACTION92
2.73-2.780.27681950.26853205X-RAY DIFFRACTION92
2.78-2.840.26911730.26243272X-RAY DIFFRACTION92
2.84-2.90.26221890.24753284X-RAY DIFFRACTION92
2.9-2.970.32651820.24793168X-RAY DIFFRACTION91
2.97-3.040.28641530.24973185X-RAY DIFFRACTION89
3.04-3.120.25181730.24733003X-RAY DIFFRACTION87
3.12-3.220.27721760.24293196X-RAY DIFFRACTION90
3.22-3.320.29541680.22813356X-RAY DIFFRACTION94
3.32-3.440.27991560.22343292X-RAY DIFFRACTION94
3.44-3.580.22971670.20793319X-RAY DIFFRACTION94
3.58-3.740.22941980.21053228X-RAY DIFFRACTION93
3.74-3.940.19691590.1933233X-RAY DIFFRACTION91
3.94-4.180.22091690.18433045X-RAY DIFFRACTION87
4.18-4.510.21651580.17213341X-RAY DIFFRACTION93
4.51-4.960.22541840.19033263X-RAY DIFFRACTION92
4.96-5.680.24971570.19823201X-RAY DIFFRACTION90
5.68-7.150.20751680.20753139X-RAY DIFFRACTION90
7.15-65.630.1881430.17882965X-RAY DIFFRACTION83
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)
16.6038-0.11070.62554.54610.5513.16020.0292-1.67220.93840.51670.03450.2696-0.32870.0454-0.06050.6962-0.0450.06520.7775-0.28820.54031.364314.446562.4353
24.50040.1651-1.1124.62991.56564.48730.2268-1.2260.06130.9069-0.30120.4025-0.2139-0.07860.09320.5073-0.0440.020.72010.01470.3475-4.75783.520663.1159
35.36510.54060.43682.95520.74037.0844-0.08490.06250.9945-0.1761-0.08180.1909-0.8950.50330.1560.3795-0.04110.04910.2147-0.00850.5243-0.076712.081442.6141
46.68381.8739-1.46521.5584-0.68463.13320.0856-0.28480.17050.110.05320.1884-0.2075-0.3413-0.14120.27830.0687-0.00770.21840.02210.315-10.43321.83443.2412
56.74371.2867-1.52354.0539-0.39664.9646-0.12080.5597-0.6121-0.2650.12680.05640.2485-0.42930.01650.347-0.0027-0.05080.281-0.00250.3092-10.651-1.797731.2512
68.3113-2.21382.49913.51412.12066.04180.3534-0.6284-0.8333-0.4544-0.18640.64460.4922-0.1916-0.56360.4922-0.0333-0.13320.4487-0.00180.719813.37551.4242.1318
78.20150.51641.96184.5778-0.15836.5949-0.11990.89150.6413-0.8894-0.0578-0.2856-0.31880.25060.11370.5393-0.0132-0.00530.3220.13370.4178-28.960432.9387-8.8581
84.68330.26361.00384.5904-1.25224.6703-0.11090.91040.327-0.72320.0092-0.2829-0.29340.51390.1270.4617-0.0475-0.01330.4510.010.2913-26.47127.7302-10.5952
94.9926-0.01111.45143.1357-1.24525.0979-0.1169-0.3413-0.18910.2260.12550.0666-0.4153-0.1355-0.04110.24350.00220.010.20710.06340.2963-26.647222.28768.5499
105.796-1.65630.14381.62090.40065.32750.0318-0.07710.3597-0.05690.2009-0.3226-0.51130.4232-0.21850.2652-0.02370.02880.20650.00370.3806-12.092921.172110.1832
117.6564-1.33120.11963.8582-0.61794.8093-0.1761-0.811-0.85150.26360.20250.15960.25760.2047-0.01230.30450.0722-0.01070.3150.07290.339-14.864813.642118.8852
128.4522-1.7174-0.39822.3792-0.75882.88580.1517-1.306-0.04820.26010.06081.5522-0.7587-1.4582-0.08060.80550.23530.07960.84720.1880.6798-33.344921.774527.5726
139.9141-4.50316.3432.2998-1.84282.129-0.1893-0.0883-0.0840.6148-0.1237-1.63750.72240.56450.06510.55020.18880.00790.66470.10310.8063-42.898820.50868.8314
148.8871-0.58561.78849.3938-1.29257.5353-0.3697-0.35620.80640.35610.21670.2012-0.2229-0.64980.11720.38570.13970.04660.43720.03060.47182.484552.082361.6411
152.92630.8781-0.11433.8570.853.20460.11450.23960.40220.27280.03140.1775-0.4518-0.8273-0.07960.32410.18990.01750.57780.12520.4440.159247.516556.8664
163.272-0.092-0.59182.6647-0.09711.64650.10820.9641-0.1137-0.3042-0.10630.3008-0.0022-0.7405-0.00020.37220.082-0.00191.05220.030.4193-11.117637.100240.2116
179.28742.04883.82260.61341.79062.40730.00260.1969-0.5125-0.404-0.03820.0343-0.2889-0.4501-0.02210.66410.11920.0180.7633-0.07620.528610.728938.307735.9193
186.5552-0.8751.08365.93941.00094.8384-0.43761.0680.7321-0.65130.04-0.3802-0.33640.90970.27290.4961-0.2145-0.06340.69650.16640.4381-31.2579-3.1157-10.3765
194.6723-1.11111.25015.2439-1.19473.5765-0.04351.2940.4267-0.7902-0.3165-0.4636-0.1720.97890.31950.5193-0.1477-0.03780.68480.04830.4281-28.222-8.0779-11.5482
205.0063-1.27030.31531.83910.05292.51820.02560.18640.1762-0.017-0.0611-0.112-0.14070.02740.02270.3097-0.0587-0.03260.2864-0.01380.3373-22.7595-12.61037.2632
213.9589-0.611-0.91073.79720.82484.65730.0464-0.50230.11230.38680.0556-0.7302-0.01570.6295-0.09540.2861-0.0245-0.0840.401-0.02840.3413-12.3548-14.507416.5298
225.8147-1.3213-3.22075.72632.94492.23-0.6592-0.2875-0.97320.7473-0.12390.58961.2844-0.14140.61990.4774-0.03750.03290.40530.07860.5819-25.7721-24.712719.1548
237.4718-1.08886.24130.4791-1.99424.93650.266-0.8094-0.27020.2030.1660.2520.17-0.5188-0.40250.5929-0.00730.05330.48750.03270.3949-39.4559-14.275416.6211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 701 through 752 )
2X-RAY DIFFRACTION2chain 'A' and (resid 753 through 786 )
3X-RAY DIFFRACTION3chain 'A' and (resid 787 through 810 )
4X-RAY DIFFRACTION4chain 'A' and (resid 811 through 919 )
5X-RAY DIFFRACTION5chain 'A' and (resid 920 through 991 )
6X-RAY DIFFRACTION6chain 'A' and (resid 992 through 1011 )
7X-RAY DIFFRACTION7chain 'B' and (resid 700 through 731 )
8X-RAY DIFFRACTION8chain 'B' and (resid 732 through 786 )
9X-RAY DIFFRACTION9chain 'B' and (resid 787 through 853 )
10X-RAY DIFFRACTION10chain 'B' and (resid 854 through 919 )
11X-RAY DIFFRACTION11chain 'B' and (resid 920 through 977 )
12X-RAY DIFFRACTION12chain 'B' and (resid 978 through 991 )
13X-RAY DIFFRACTION13chain 'B' and (resid 992 through 1008 )
14X-RAY DIFFRACTION14chain 'C' and (resid 700 through 731 )
15X-RAY DIFFRACTION15chain 'C' and (resid 732 through 810 )
16X-RAY DIFFRACTION16chain 'C' and (resid 811 through 977 )
17X-RAY DIFFRACTION17chain 'C' and (resid 978 through 1008 )
18X-RAY DIFFRACTION18chain 'D' and (resid 700 through 731 )
19X-RAY DIFFRACTION19chain 'D' and (resid 732 through 790 )
20X-RAY DIFFRACTION20chain 'D' and (resid 791 through 892 )
21X-RAY DIFFRACTION21chain 'D' and (resid 893 through 960 )
22X-RAY DIFFRACTION22chain 'D' and (resid 961 through 977 )
23X-RAY DIFFRACTION23chain 'D' and (resid 978 through 1008 )

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