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- PDB-7jxk: EGFR kinase (T790M/V948R) in complex with PF-06747775 and JBJ-04-... -

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Basic information

Entry
Database: PDB / ID: 7jxk
TitleEGFR kinase (T790M/V948R) in complex with PF-06747775 and JBJ-04-125-02
ComponentsEpidermal growth factor receptor
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / EGFR / ErbB1 / kinase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Developmental Lineage of Mammary Gland Myoepithelial Cells / 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 ...multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Developmental Lineage of Mammary Gland Myoepithelial Cells / 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 / ubiquitin-dependent endocytosis / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / Signaling by EGFR / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / intracellular vesicle / eyelid development in camera-type eye / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / protein insertion into membrane / negative regulation of epidermal growth factor receptor signaling pathway / 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 / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / embryonic placenta development / xenobiotic transport / salivary gland morphogenesis / positive regulation of epidermal growth factor receptor signaling pathway / sperm end piece / 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 / SHC1 events in ERBB2 signaling / sperm principal piece / ossification / basal plasma membrane / cellular response to epidermal growth factor stimulus / epithelial cell proliferation / positive regulation of DNA replication / positive regulation of DNA repair / positive regulation of epithelial cell proliferation / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to estradiol stimulus / cellular response to amino acid stimulus / clathrin-coated endocytic vesicle membrane / EGFR downregulation / Signaling by ERBB2 TMD/JMD mutants / cell-cell adhesion / Constitutive Signaling by EGFRvIII / 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 / epidermal growth factor receptor signaling pathway / kinase binding / Downregulation of ERBB2 signaling / ruffle membrane / positive regulation of fibroblast proliferation / cell morphogenesis / positive regulation of protein phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / neuron differentiation / HCMV Early Events / actin filament binding / transmembrane signaling receptor activity / cell junction / positive regulation of canonical Wnt signaling pathway / sperm midpiece / PIP3 activates AKT signaling / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / virus receptor activity / positive regulation of cell growth / RAF/MAP kinase cascade / protein tyrosine kinase activity / double-stranded DNA binding / early 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-8BS / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-JBJ / Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBeyett, T.S. / Eck, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA201049-05 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)1F32CA247198-01 United States
CitationJournal: Nat Commun / Year: 2022
Title: Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors
Authors: Beyett, T.S. / To, C. / Heppner, D.E. / Rana, J.K. / Schmoker, A.M. / Jang, J. / De Clercq, D.J.H. / Gomez, G. / Scott, D.A. / Gray, N.S. / Janne, P.A. / Eck, M.J.
History
DepositionAug 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 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
D: Epidermal growth factor receptor
A: Epidermal growth factor receptor
C: Epidermal growth factor receptor
F: Epidermal growth factor receptor
E: Epidermal growth factor receptor
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,79619
Polymers226,3486
Non-polymers5,44913
Water00
1
D: Epidermal growth factor receptor
A: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4847
Polymers75,4492
Non-polymers2,0355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-31 kcal/mol
Surface area25930 Å2
MethodPISA
2
C: Epidermal growth factor receptor
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9416
Polymers75,4492
Non-polymers1,4924
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-31 kcal/mol
Surface area26330 Å2
MethodPISA
3
E: Epidermal growth factor receptor
hetero molecules

F: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3716
Polymers75,4492
Non-polymers1,9224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3170 Å2
ΔGint-19 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.853, 87.369, 91.313
Angle α, β, γ (deg.)62.060, 85.580, 73.330
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 701 through 857 or resid 876...
21(chain B and (resid 701 through 907 or resid 909 through 984 or resid 990 through 1007))
31(chain C and (resid 701 through 857 or resid 876...
41(chain D and (resid 701 through 857 or resid 876...
51(chain E and (resid 701 through 857 or resid 876 through 907 or resid 909 through 1007))
61(chain F and (resid 701 through 857 or resid 876...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLYGLY(chain A and (resid 701 through 857 or resid 876...AB701 - 85710 - 166
12VALVALLEULEU(chain A and (resid 701 through 857 or resid 876...AB876 - 907185 - 216
13THRTHRASPASP(chain A and (resid 701 through 857 or resid 876...AB909 - 984218 - 293
14PROPROMETMET(chain A and (resid 701 through 857 or resid 876...AB990 - 1007299 - 316
21GLNGLNLEULEU(chain B and (resid 701 through 907 or resid 909 through 984 or resid 990 through 1007))BF701 - 90710 - 216
22THRTHRASPASP(chain B and (resid 701 through 907 or resid 909 through 984 or resid 990 through 1007))BF909 - 984218 - 293
23PROPROMETMET(chain B and (resid 701 through 907 or resid 909 through 984 or resid 990 through 1007))BF990 - 1007299 - 316
31GLNGLNGLYGLY(chain C and (resid 701 through 857 or resid 876...CC701 - 85710 - 166
32VALVALLEULEU(chain C and (resid 701 through 857 or resid 876...CC876 - 907185 - 216
33THRTHRASPASP(chain C and (resid 701 through 857 or resid 876...CC909 - 984218 - 293
34PROPROMETMET(chain C and (resid 701 through 857 or resid 876...CC990 - 1007299 - 316
41GLNGLNGLYGLY(chain D and (resid 701 through 857 or resid 876...DA701 - 85710 - 166
42VALVALLEULEU(chain D and (resid 701 through 857 or resid 876...DA876 - 907185 - 216
43THRTHRASPASP(chain D and (resid 701 through 857 or resid 876...DA909 - 984218 - 293
44PROPROMETMET(chain D and (resid 701 through 857 or resid 876...DA990 - 1007299 - 316
51GLNGLNGLYGLY(chain E and (resid 701 through 857 or resid 876 through 907 or resid 909 through 1007))EE701 - 85710 - 166
52VALVALLEULEU(chain E and (resid 701 through 857 or resid 876 through 907 or resid 909 through 1007))EE876 - 907185 - 216
53THRTHRMETMET(chain E and (resid 701 through 857 or resid 876 through 907 or resid 909 through 1007))EE909 - 1007218 - 316
61GLNGLNGLYGLY(chain F and (resid 701 through 857 or resid 876...FD701 - 85710 - 166
62VALVALLEULEU(chain F and (resid 701 through 857 or resid 876...FD876 - 907185 - 216
63THRTHRASPASP(chain F and (resid 701 through 857 or resid 876...FD909 - 984218 - 293
64PROPROMETMET(chain F and (resid 701 through 857 or resid 876...FD990 - 1007299 - 316

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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.: 6 / 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 / Plasmid: pTriEX / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-JBJ / (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{1-oxo-6-[4-(piperazin-1-yl)phenyl]-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide


Mass: 543.612 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C29H26FN5O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-8BS / N-[(3R,4R)-4-fluoro-1-{6-[(3-methoxy-1-methyl-1H-pyrazol-4-yl)amino]-9-methyl-9H-purin-2-yl}pyrrolidin-3-yl]propanamide


Mass: 417.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H24FN9O2 / Feature type: SUBJECT OF INVESTIGATION
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

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: 0.9778 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.1→80.48 Å / Num. obs: 28896 / % possible obs: 91.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 59.31 Å2 / Rpim(I) all: 0.094 / Rrim(I) all: 0.183 / Net I/σ(I): 8 / Num. measured all: 106143
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
3.1-3.153.51493114170.651.25389.9
8.41-80.513.830.3546214500.0220.04392

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D41

5d41


Resolution: 3.1→80.48 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2609 1453 5.05 %
Rwork0.2215 27293 -
obs0.2234 28746 90.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.36 Å2 / Biso mean: 76.7694 Å2 / Biso min: 27.75 Å2
Refinement stepCycle: final / Resolution: 3.1→80.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14098 0 379 0 14477
Biso mean--81.02 --
Num. residues----1748
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8563X-RAY DIFFRACTION9.383TORSIONAL
12B8563X-RAY DIFFRACTION9.383TORSIONAL
13C8563X-RAY DIFFRACTION9.383TORSIONAL
14D8563X-RAY DIFFRACTION9.383TORSIONAL
15E8563X-RAY DIFFRACTION9.383TORSIONAL
16F8563X-RAY DIFFRACTION9.383TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.210.35871660.29732727289391
3.21-3.340.31361470.26052806295393
3.34-3.490.32411130.25532810292393
3.49-3.680.26081480.2482701284990
3.68-3.910.30741310.2332614274587
3.91-4.210.25671790.20322795297494
4.21-4.630.17881450.19162755290092
4.63-5.30.23991420.2112618276087
5.3-6.680.23511320.21932822295493
6.68-80.480.26831500.19962645279589
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)
12.78491.793-0.13276.4268-0.26882.2307-0.004-0.3131-0.44580.0406-0.1364-0.12650.13080.24910.12730.31940.06750.0950.42350.02320.394114.50745.896-33.596
23.99052.1893-0.75185.8471-0.67022.5333-0.13680.04320.303-0.4050.08830.0504-0.2646-0.08920.05560.33570.062-0.03860.2602-0.06410.384521.9682.76-45.778
33.0622-0.9782-0.35199.50760.09272.5661-0.1344-0.3613-0.82580.18640.16371.10960.26260.04220.06450.3791-0.03050.05720.4840.050.703433.05932.568-61.528
45.46772.0448-0.56142.9803-0.54911.86840.1202-0.11010.34830.117-0.06080.3133-0.3841-0.1842-0.0250.45940.07730.02980.2869-0.07570.404245.38413.984-21.462
53.85541.4259-2.00497.8539-1.03663.7931-0.3509-0.2966-0.7375-0.24520.02050.06840.7116-0.30640.34630.3966-0.04890.11520.49070.03090.520259.52962.467-7.233
62.30150.45860.265611.5354-0.99382.9833-0.08380.22840.2281-2.24870.01770.2291-0.24690.12070.06560.9924-0.071-0.10980.5033-0.05140.285539.869.811-73.421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND ( RESID 700:1007 OR RESID 1101:1103 ) )D700 - 1007
2X-RAY DIFFRACTION1( CHAIN D AND ( RESID 700:1007 OR RESID 1101:1103 ) )D1101 - 1103
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 700:1007 OR RESID 1101:1102 ) )A700 - 1007
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 700:1007 OR RESID 1101:1102 ) )A1101 - 1102
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 701:1007 OR RESID 1101:1102 ) )C701 - 1007
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 701:1007 OR RESID 1101:1102 ) )C1101 - 1102
7X-RAY DIFFRACTION4( CHAIN F AND ( RESID 700:1007 OR RESID 1101:1102 ) )F700 - 1007
8X-RAY DIFFRACTION4( CHAIN F AND ( RESID 700:1007 OR RESID 1101:1102 ) )F1101 - 1102
9X-RAY DIFFRACTION5( CHAIN E AND ( RESID 700:1007 OR RESID 1101:1102 ) )E700 - 1007
10X-RAY DIFFRACTION5( CHAIN E AND ( RESID 700:1007 OR RESID 1101:1102 ) )E1101 - 1102
11X-RAY DIFFRACTION6( CHAIN B AND ( RESID 700:1007 OR RESID 1101:1101 ) )B700 - 1007
12X-RAY DIFFRACTION6( CHAIN B AND ( RESID 700:1007 OR RESID 1101:1101 ) )B1101

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