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- PDB-7a6k: Crystal Structure of EGFR-T790M/V948R in Complex with TAK-788 -

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Basic information

Entry
Database: PDB / ID: 7a6k
TitleCrystal Structure of EGFR-T790M/V948R in Complex with TAK-788
ComponentsEpidermal growth factor receptor
KeywordsTRANSFERASE / EGFR / T790M/V948R / Exon20 / covalent
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 / EGFR interacts with phospholipase C-gamma / epidermal growth factor receptor activity / 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 / EGFR interacts with phospholipase C-gamma / epidermal growth factor receptor activity / 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 / eyelid development in camera-type eye / negative regulation of epidermal growth factor receptor signaling pathway / 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 / GRB2 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SHC1 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / ossification / NOTCH3 Activation and Transmission of Signal to the Nucleus / positive regulation of DNA repair / basal plasma membrane / cellular response to epidermal growth factor stimulus / EGFR downregulation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / positive regulation of epithelial cell proliferation / positive regulation of protein localization to plasma membrane / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Downregulation of ERBB2 signaling / cell-cell adhesion / receptor protein-tyrosine kinase / negative regulation of protein catabolic process / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of miRNA transcription / kinase binding / ruffle membrane / positive regulation of protein phosphorylation / epidermal growth factor receptor signaling pathway / neuron differentiation / cell morphogenesis / positive regulation of fibroblast proliferation / HCMV Early Events / Constitutive Signaling by Aberrant PI3K in Cancer / actin filament binding / Cargo recognition for clathrin-mediated endocytosis / cell junction / transmembrane signaling receptor activity / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / positive regulation of canonical Wnt signaling pathway / Clathrin-mediated endocytosis / PIP3 activates AKT signaling / virus receptor activity / ATPase binding / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 / endosome membrane
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-R28 / Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNiggenaber, J. / Mueller, M.P. / Rauh, D.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchBMBF 01GS08104 Germany
German Federal Ministry for Education and ResearchBMBF 01ZX1303C Germany
European Regional Development FundEFRE-800400 Germany
CitationJournal: J.Med.Chem. / Year: 2022
Title: Insight into Targeting Exon20 Insertion Mutations of the Epidermal Growth Factor Receptor with Wild Type-Sparing Inhibitors.
Authors: Lategahn, J. / Tumbrink, H.L. / Schultz-Fademrecht, C. / Heimsoeth, A. / Werr, L. / Niggenaber, J. / Keul, M. / Parmaksiz, F. / Baumann, M. / Menninger, S. / Zent, E. / Landel, I. / Weisner, ...Authors: Lategahn, J. / Tumbrink, H.L. / Schultz-Fademrecht, C. / Heimsoeth, A. / Werr, L. / Niggenaber, J. / Keul, M. / Parmaksiz, F. / Baumann, M. / Menninger, S. / Zent, E. / Landel, I. / Weisner, J. / Jeyakumar, K. / Heyden, L. / Russ, N. / Muller, F. / Lorenz, C. / Bragelmann, J. / Spille, I. / Grabe, T. / Muller, M.P. / Heuckmann, J.M. / Klebl, B.M. / Nussbaumer, P. / Sos, M.L. / Rauh, D.
History
DepositionAug 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 5, 2022Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 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)154,87915
Polymers151,8564
Non-polymers3,02311
Water2,468137
1
A: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5522
Polymers37,9641
Non-polymers5881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6483
Polymers37,9641
Non-polymers6842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9366
Polymers37,9641
Non-polymers9725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7444
Polymers37,9641
Non-polymers7803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.100, 82.420, 90.000
Angle α, β, γ (deg.)90.000, 90.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37963.910 Da / Num. of mol.: 4 / 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-R28 / propan-2-yl 2-[[4-[2-(dimethylamino)ethyl-methyl-amino]-2-methoxy-5-(propanoylamino)phenyl]amino]-4-(1-methylindol-3-yl)pyrimidine-5-carboxylate / Mobocertinib, bound form


Mass: 587.712 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H41N7O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.76 Å3/Da / Density % sol: 29.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25.0 % PEG3350, 100 mM MgSO4, 4 % ethylen glycole, 6.8 mg/mL EGFR-T790M/V948R (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP, pH 8.0) 1 ul reservoir + 1 ul protein solution)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 5, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2→47.49 Å / Num. obs: 74127 / % possible obs: 99.9 % / Redundancy: 6.81 % / CC1/2: 0.999 / Rrim(I) all: 0.078 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.94 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10013 / CC1/2: 0.751 / Rrim(I) all: 0.961 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S8A

6s8a


Resolution: 2→47.49 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.71
RfactorNum. reflection% reflection
Rfree0.2202 3706 5 %
Rwork0.1919 --
obs0.1933 74112 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.45 Å2 / Biso mean: 51.6092 Å2 / Biso min: 24.12 Å2
Refinement stepCycle: final / Resolution: 2→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8071 0 207 137 8415
Biso mean--48.1 46.65 -
Num. residues----1043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.31351420.307426842826100
2.03-2.050.32291390.291526572796100
2.05-2.080.29221440.283127332877100
2.08-2.110.30771410.264726792820100
2.11-2.150.26211430.247427142857100
2.15-2.180.27031410.229626752816100
2.18-2.220.22481440.22627282872100
2.22-2.260.23731400.223226772817100
2.26-2.30.23441420.216126872829100
2.3-2.350.24861430.217427122855100
2.35-2.40.25641400.217426662806100
2.4-2.460.23531420.217426962838100
2.46-2.520.27561440.228227362880100
2.52-2.590.26981440.223127322876100
2.59-2.660.25271410.221926852826100
2.66-2.750.2521420.221226902832100
2.75-2.850.26341430.218627242867100
2.85-2.960.24961410.221126812822100
2.96-3.10.24311440.22327332877100
3.1-3.260.23061420.216626972839100
3.26-3.460.25631430.194627232866100
3.46-3.730.1991430.172527072850100
3.73-4.110.21181440.15527272871100
4.11-4.70.16281440.143527402884100
4.7-5.920.18421430.164627322875100
5.92-47.490.19161470.1762791293899
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)
10.6458-0.46290.40440.7126-1.28933.4639-0.04820.07290.0773-0.6301-0.09170.35360.0716-0.0897-0.02160.4389-0.10050.02790.65620.02650.3808-2.15734.004715.3584
22.29170.2434.09514.3131-0.66227.7629-0.33461.1851-0.0301-0.4452-0.0606-0.6903-0.15441.32090.34250.4396-0.03930.11580.65280.09130.41796.444411.578419.0356
30.522-0.2415-0.33681.23370.66311.2706-0.18451.0173-0.1603-0.51-0.12660.17310.15410.01720.05640.4814-0.03020.03880.650.00770.43580.52355.447515.7451
41.97030.78531.05361.68580.07044.8185-0.07590.2269-0.0225-0.0973-0.0797-0.08920.02150.10490.11120.16830.010.00490.22380.01330.26532.79656.928933.2264
53.731-1.05060.2224.31891.24852.5489-0.14080.11690.14340.1430.0319-0.38470.00970.32580.09860.2916-0.04-0.03950.32180.08230.385117.87186.35844.1653
64.63381.2632-0.91922.4123-0.25953.169-0.1649-0.42490.42611.1567-0.22210.7152-0.1819-0.07120.28730.4457-0.0049-0.04970.3754-0.02050.44442.576112.595253.2404
73.28252.090.24794.75770.52434.9389-0.55930.92340.8227-0.90890.44080.4088-0.27160.41320.00230.4847-0.152-0.15160.58320.08650.440834.0039-5.358661.6123
81.92971.847-1.22432.8573-0.20734.8917-0.530.98230.732-0.57840.1920.1875-0.51090.2456-0.06780.5735-0.227-0.01740.54720.03030.334736.3873-5.37860.844
92.43261.426-0.0542.34610.08534.6527-0.15220.07330.179-0.17170.04140.1895-0.18370.09720.01730.19020.0253-0.01960.19350.00410.295833.1844-6.066377.4931
101.77051.3047-0.24124.59340.93384.5490.12020.41020.3268-0.4072-0.13920.1223-0.1475-0.22090.0560.26280.02290.05920.27590.01730.377630.5806-5.373980.1784
114.4141-0.84620.35755.3563-0.89742.7387-0.0310.1582-0.0239-0.0699-0.03020.3634-0.1201-0.3779-0.00770.31360.01230.04260.3691-0.05290.340216.3307-6.176587.2064
125.0194-1.13760.38166.3156-1.64922.90520.0199-0.67180.03360.7055-0.06120.0962-0.2007-0.02740.12620.3689-0.04590.04790.3959-0.05190.237426.6276-7.32898.1765
131.87380.04210.4285.22270.22082.1539-0.14750.11230.2089-0.31840.1861-0.0453-0.32490.158-0.03420.2407-0.05250.00460.2743-0.00250.262816.1709-30.304456.8209
146.36691.32-0.76322.49660.38693.4401-0.13080.1143-0.286-0.1730.1918-0.29180.02980.3317-0.05610.30480.0267-0.01190.2816-0.04470.380128.0866-49.965557.9337
153.08172.00451.57594.71180.31722.1805-0.08980.0744-0.46360.12470.2540.03210.3628-0.048-0.00030.49130.1430.07910.3942-0.0260.5962-22.6037-22.104577.0107
162.2372.2943-2.63077.6837-1.95953.745-0.3149-0.4467-0.81050.31530.38931.13790.772-0.36810.11980.65280.10070.16390.37610.06630.6406-27.3802-21.991476.6069
171.39420.93590.86831.1871-0.25372.01020.5079-0.6822-0.20580.97490.1451-0.54781.0340.7917-0.02380.86570.1957-0.08250.70050.00060.491-21.8396-14.745491.757
183.42940.5492-0.3457.2626-0.27422.8852-0.14760.0972-0.0065-0.0030.22960.01580.16350.1794-0.05610.21320.0349-0.02280.3391-0.02120.2404-22.2587-4.232175.4952
194.46680.8205-2.36995.0891.58876.80620.0701-0.6775-0.40220.54150.2234-0.44590.56810.7271-0.02560.41760.0446-0.01990.40550.00710.2673-19.9131-2.655778.8573
202.4786-2.04661.2121.6598-0.88253.2527-0.6287-1.72490.05890.94820.40630.24130.94921.02830.15090.61030.3082-0.07311.0848-0.17960.6273-5.29670.434685.0107
216.697-0.652-1.31822.7520.89772.9632-0.1292-0.34221.11780.09270.2692-0.4888-0.17330.5791-0.12350.27370.0017-0.03410.4304-0.07940.5288-11.301511.459875.4308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 700 through 717 )A700 - 717
2X-RAY DIFFRACTION2chain 'A' and (resid 718 through 731 )A718 - 731
3X-RAY DIFFRACTION3chain 'A' and (resid 732 through 758 )A732 - 758
4X-RAY DIFFRACTION4chain 'A' and (resid 759 through 853 )A759 - 853
5X-RAY DIFFRACTION5chain 'A' and (resid 854 through 960 )A854 - 960
6X-RAY DIFFRACTION6chain 'A' and (resid 961 through 984 )A961 - 984
7X-RAY DIFFRACTION7chain 'B' and (resid 700 through 731 )B700 - 731
8X-RAY DIFFRACTION8chain 'B' and (resid 732 through 757 )B732 - 757
9X-RAY DIFFRACTION9chain 'B' and (resid 758 through 830 )B758 - 830
10X-RAY DIFFRACTION10chain 'B' and (resid 831 through 853 )B831 - 853
11X-RAY DIFFRACTION11chain 'B' and (resid 854 through 940 )B854 - 940
12X-RAY DIFFRACTION12chain 'B' and (resid 941 through 982 )B941 - 982
13X-RAY DIFFRACTION13chain 'C' and (resid 700 through 853 )C700 - 853
14X-RAY DIFFRACTION14chain 'C' and (resid 854 through 984 )C854 - 984
15X-RAY DIFFRACTION15chain 'D' and (resid 702 through 731 )D702 - 731
16X-RAY DIFFRACTION16chain 'D' and (resid 732 through 756 )D732 - 756
17X-RAY DIFFRACTION17chain 'D' and (resid 757 through 768 )D757 - 768
18X-RAY DIFFRACTION18chain 'D' and (resid 769 through 830 )D769 - 830
19X-RAY DIFFRACTION19chain 'D' and (resid 831 through 853 )D831 - 853
20X-RAY DIFFRACTION20chain 'D' and (resid 854 through 892 )D854 - 892
21X-RAY DIFFRACTION21chain 'D' and (resid 893 through 984 )D893 - 984

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