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- PDB-8gb4: EGFR(T790M/V948R) kinase in complex with benzimidazole allosteric... -

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Basic information

Entry
Database: PDB / ID: 8gb4
TitleEGFR(T790M/V948R) kinase in complex with benzimidazole allosteric inhibitor
ComponentsEpidermal growth factor receptor
KeywordsTRANSFERASE / EGFR / kinase / allosteric / inhibitor / cancer
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 / transmembrane receptor protein tyrosine kinase activity / SHC1 events in EGFR signaling / 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 / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / positive regulation of miRNA transcription / kinase binding / ruffle membrane / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / positive regulation of protein phosphorylation / positive regulation of fibroblast proliferation / cell morphogenesis / 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 / cell surface receptor signaling pathway / Extra-nuclear estrogen signaling / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBeyett, T.S. / Eck, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA116020-16 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA201049-08 United States
CitationJournal: To be published
Title: EGFR(T790M/V948R) kinase in complex with benzimidazole allosteric inhibitor
Authors: Beyett, T.S. / Eck, M.J.
History
DepositionFeb 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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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)155,14316
Polymers150,8984
Non-polymers4,24512
Water2,000111
1
A: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7864
Polymers37,7251
Non-polymers1,0613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7864
Polymers37,7251
Non-polymers1,0613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7864
Polymers37,7251
Non-polymers1,0613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7864
Polymers37,7251
Non-polymers1,0613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.450, 73.450, 118.419
Angle α, β, γ (deg.)90.00, 118.45, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 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: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.59→104.11 Å / Num. obs: 39094 / % possible obs: 98 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.094 / Rrim(I) all: 0.186 / Net I/σ(I): 6.1 / Num. measured all: 145559
Reflection shellResolution: 2.59→2.64 Å / % possible obs: 92.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.947 / Num. measured all: 6539 / Num. unique obs: 1847 / CC1/2: 0.516 / Rpim(I) all: 0.568 / Rrim(I) all: 1.11 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
DIALSdata scaling
PHENIX1.20.1refinement
DIALSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→104.11 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 1908 4.92 %
Rwork0.2291 --
obs0.2303 38756 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→104.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9439 0 288 111 9838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049986
X-RAY DIFFRACTIONf_angle_d0.66813553
X-RAY DIFFRACTIONf_dihedral_angle_d13.5763787
X-RAY DIFFRACTIONf_chiral_restr0.0491490
X-RAY DIFFRACTIONf_plane_restr0.0041666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.660.3331240.30912372X-RAY DIFFRACTION88
2.66-2.730.33361280.29852615X-RAY DIFFRACTION96
2.73-2.810.34481460.29362498X-RAY DIFFRACTION95
2.81-2.90.29311380.27482665X-RAY DIFFRACTION98
2.9-3.010.2961320.26712646X-RAY DIFFRACTION99
3.01-3.130.36211380.25822668X-RAY DIFFRACTION99
3.13-3.270.28561570.24652668X-RAY DIFFRACTION99
3.27-3.440.28151180.24752685X-RAY DIFFRACTION98
3.44-3.660.28771320.2322609X-RAY DIFFRACTION96
3.66-3.940.23951150.21192676X-RAY DIFFRACTION99
3.94-4.340.22091500.20032681X-RAY DIFFRACTION99
4.34-4.960.23341230.19532723X-RAY DIFFRACTION99
4.96-6.250.21971470.2162635X-RAY DIFFRACTION97
6.25-104.110.17361600.19822707X-RAY DIFFRACTION97
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)
14.588-1.7206-0.20088.0028-3.37167.3436-0.017-0.27590.29650.63720.25320.2444-0.7977-0.1829-0.31020.32730.0210.09080.2917-0.06330.36712.759746.899761.4439
29.49120.07-1.00483.0391-0.16044.537-0.4185-0.5721.21440.82670.5560.2564-0.4987-0.5470.01540.58410.1220.06570.3067-0.04520.52444.669848.549362.7803
38.1197-2.8186-4.18377.95944.73168.5112-0.3471-0.4119-0.15750.67770.34421.307-0.5341-1.1265-0.02920.62770.10470.15570.61460.23450.5326-8.607537.715967.6847
45.60330.663-0.60214.56071.81715.97030.20890.34980.70270.1633-0.1322-0.2178-0.7833-0.3563-0.24220.33460.06640.01880.26040.13650.46260.239838.703960.1836
56.68610.45942.37453.71923.24547.7409-0.40630.60130.7162-0.72640.294-0.3188-1.21670.2958-0.03510.4002-0.01620.12860.44210.07940.51722.618943.084738.7957
64.2525-0.27151.15313.07980.3964.06720.14620.0197-0.40680.04450.03840.2814-0.3011-0.2985-0.10760.23010.05710.02210.312-0.00850.3235-2.134331.522845.2152
73.9821-0.68951.19471.17290.17591.1847-0.1123-0.4035-0.0262-0.0735-0.081-0.0773-0.3153-0.67820.18980.39370.0740.05720.6497-0.01340.5238-18.313835.742848.7645
81.5227-0.0323-0.61824.3718-1.15224.53180.10490.4042-0.0297-0.37890.04280.66760.0085-0.5803-0.11520.28320.0723-0.05820.55920.01290.3882-15.875833.002735.6598
92.8144-0.8594-0.29555.0317-1.58276.93860.05060.6705-0.064-0.9089-0.3404-0.68730.43930.5040.19190.420.09250.030.6419-0.12220.45441.099727.361530.1726
105.78332.7416-1.48268.2555-0.76695.59870.3821-0.9989-0.1553-0.3311-0.7461.57320.486-0.13460.53120.4477-0.07690.0520.6334-0.10540.689715.590933.014244.4892
115.2641-0.11470.13947.6027-0.18862.95380.0359-0.78470.97650.8055-0.00360.55990.09180.022-0.17750.41030.06950.05930.5834-0.20860.57550.93381.501761.6238
123.2756-0.1554-0.0954.45020.52032.30030.0357-0.86440.29680.5911-0.0740.4683-0.0032-0.32290.05240.5730.04080.09210.7058-0.07170.3235-2.216677.952664.7099
134.51190.64511.19232.52681.576.0069-0.0072-0.18090.21150.06-0.00290.0982-0.4345-0.2044-0.00020.17640.0548-0.00260.23780.03430.3365-1.477572.170646.67
147.23593.4492-3.03616.0315-2.71764.04640.1903-0.11650.39170.60110.08750.7812-0.4648-0.2988-0.31270.30430.06390.02470.3329-0.02130.3379-19.224969.637347.8497
156.7157-0.1346-0.0545.242-1.06586.19060.07520.5592-0.199-0.03580.06330.00880.2199-0.5461-0.1160.2933-0.04470.00370.3088-0.01120.2213-13.676367.002533.9857
167.2180.29924.96350.06710.33433.56950.29330.53520.1905-0.0601-0.242-0.310.30140.4605-0.13130.48630.1092-0.00850.4936-0.0290.579410.755372.31634.8362
177.2864-1.81422.53365.0875-0.41715.2388-0.2830.64830.8906-0.84310.1763-0.7781-0.05760.20960.220.448-0.1530.01070.46720.03770.4617-31.101265.5923-10.2161
185.8623-0.88742.20334.8938-0.63334.6367-0.04331.03070.4706-0.82680.0084-0.5749-0.19320.90260.01420.3917-0.15740.05150.5837-0.06850.4192-28.027560.456-11.3761
193.9106-1.42720.82783.1474-0.13662.8484-0.1039-0.3335-0.02090.06520.19980.1252-0.2850.09-0.07740.2445-0.0716-0.00930.3424-0.00730.3398-27.59155.47558.8951
202.6921-0.86110.98131.6798-0.17320.92490.20230.46680.2926-0.40910.2071-0.844-0.40630.6459-0.02280.388-0.06630.03080.5262-0.05330.6056-9.945855.03953.1382
211.55940.0746-1.14783.29120.34723.9925-0.1609-0.58010.33150.49410.4029-0.9320.29090.8787-0.28250.30280.0057-0.05540.6286-0.09980.5645-12.238353.255316.394
221.8235-0.81331.3251.41240.18633.2227-0.2438-0.6141-0.75530.60330.00660.91920.2087-0.38870.11820.4886-0.16620.10290.60750.14320.5077-29.344848.669222.5288
232.0072-2.8451-0.50121.2232.24729.16180.05220.044-1.20160.47290.031-0.12180.80940.81190.19840.5323-0.1582-0.10110.6999-0.00510.5713-42.508751.68799.1502
247.9007-1.54632.12114.4789-1.38238.26250.12080.72640.6012-0.5512-0.07910.0115-0.5730.0580.08340.3886-0.05280.06160.27760.10070.5248-28.6902101.6194-8.7443
252.96931.50870.69624.63792.01274.7513-0.07861.4332-0.0541-0.5710.177-0.6619-0.17480.8093-0.06760.57960.04780.05620.74310.07520.3807-25.579298.4191-12.0963
266.1547-1.72811.30592.6336-1.24746.9502-0.0092-0.1651-0.23860.04240.16110.1363-0.5236-0.1694-0.1290.23280.02040.00590.1780.03230.3279-26.67490.92415.3715
272.0335-3.96750.62732.3660.22561.45030.07570.77270.5795-0.0063-0.1065-0.0949-0.37750.45550.17020.3202-0.06030.01540.35320.01490.294-9.016388.07043.9867
287.7111-0.5697-0.8143.23280.42336.7543-0.0193-0.9493-0.38840.42380.2349-0.08010.17460.5814-0.15670.30250.0865-0.03610.38330.07630.3139-14.843684.405717.7733
297.9717-1.10345.71240.3914-1.46725.5538-0.5833-0.48650.13860.1572-0.00890.5678-0.8501-0.48630.58930.62550.275-0.03620.79260.03070.7062-38.904790.355216.8919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 700 through 731 )
2X-RAY DIFFRACTION2chain 'A' and (resid 732 through 752 )
3X-RAY DIFFRACTION3chain 'A' and (resid 753 through 766 )
4X-RAY DIFFRACTION4chain 'A' and (resid 767 through 790 )
5X-RAY DIFFRACTION5chain 'A' and (resid 791 through 810 )
6X-RAY DIFFRACTION6chain 'A' and (resid 811 through 853 )
7X-RAY DIFFRACTION7chain 'A' and (resid 854 through 892 )
8X-RAY DIFFRACTION8chain 'A' and (resid 893 through 960 )
9X-RAY DIFFRACTION9chain 'A' and (resid 961 through 991 )
10X-RAY DIFFRACTION10chain 'A' and (resid 992 through 1007 )
11X-RAY DIFFRACTION11chain 'B' and (resid 700 through 731 )
12X-RAY DIFFRACTION12chain 'B' and (resid 732 through 766 )
13X-RAY DIFFRACTION13chain 'B' and (resid 767 through 853 )
14X-RAY DIFFRACTION14chain 'B' and (resid 854 through 892 )
15X-RAY DIFFRACTION15chain 'B' and (resid 893 through 978 )
16X-RAY DIFFRACTION16chain 'B' and (resid 979 through 1007 )
17X-RAY DIFFRACTION17chain 'C' and (resid 700 through 731 )
18X-RAY DIFFRACTION18chain 'C' and (resid 732 through 790 )
19X-RAY DIFFRACTION19chain 'C' and (resid 791 through 853 )
20X-RAY DIFFRACTION20chain 'C' and (resid 854 through 892 )
21X-RAY DIFFRACTION21chain 'C' and (resid 893 through 960 )
22X-RAY DIFFRACTION22chain 'C' and (resid 961 through 991 )
23X-RAY DIFFRACTION23chain 'C' and (resid 992 through 1012 )
24X-RAY DIFFRACTION24chain 'D' and (resid 700 through 731 )
25X-RAY DIFFRACTION25chain 'D' and (resid 732 through 766 )
26X-RAY DIFFRACTION26chain 'D' and (resid 767 through 853 )
27X-RAY DIFFRACTION27chain 'D' and (resid 854 through 892 )
28X-RAY DIFFRACTION28chain 'D' and (resid 893 through 978 )
29X-RAY DIFFRACTION29chain 'D' and (resid 979 through 1007 )

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