8gk5

EGFR(T790M/V948R) kinase in complex with osimertinib and benzimidazole allosteric inhibitor

Method: X-RAY DIFFRACTION Dmax: 122.2 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Epidermal growth factor receptor

Homo sapiens

UniProt P00533

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 695–1022 Fragment:kinase domain Mutation:T790M, V948R Q6K ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide × 1 YW5 2-[(R)-(1H-benzimidazol-2-yl)(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-2,3-dihydro-1H-isoindol-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;293 K;0.1 M Bis-Tris pH 5.7, 30% (w/v) PEG 3350 Resolution 2.30 Å R-free 0.252
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 695–1022 Fragment:kinase domain Mutation:T790M, V948R Q6K ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide × 1 YW5 2-[(R)-(1H-benzimidazol-2-yl)(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-2,3-dihydro-1H-isoindol-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;293 K;0.1 M Bis-Tris pH 5.7, 30% (w/v) PEG 3350 Resolution 2.30 Å R-free 0.252
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 695–1022 Fragment:kinase domain Mutation:T790M, V948R Q6K ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide × 1 YW5 2-[(R)-(1H-benzimidazol-2-yl)(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-2,3-dihydro-1H-isoindol-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;293 K;0.1 M Bis-Tris pH 5.7, 30% (w/v) PEG 3350 Resolution 2.30 Å R-free 0.252
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 695–1022 Fragment:kinase domain Mutation:T790M, V948R Q6K ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide × 1 YW5 2-[(R)-(1H-benzimidazol-2-yl)(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-2,3-dihydro-1H-isoindol-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;293 K;0.1 M Bis-Tris pH 5.7, 30% (w/v) PEG 3350 Resolution 2.30 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

383 other PDB entries and 562 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGFR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–331; UniProt 695–1022 Author chain B; PDBConstruct 4–331; UniProt 695–1022 Author chain C; PDBConstruct 4–331; UniProt 695–1022 Author chain D; PDBConstruct 4–331; UniProt 695–1022

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8gk5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8gk5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8gk5
Deposition date deposition_date2023-03-17
Structure title titleEGFR(T790M/V948R) kinase in complex with osimertinib and benzimidazole allosteric inhibitor
Keywords keywordsEGFR, kinase, covalent, inhibitor, allosteric, cancer, TRANSFERASE, TRANSFERASE-INHIBITOR complex; TRANSFERASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.10
Radius of gyration Rg (electron density) rg_electron35.97
Forward intensity I(0) i0272628000.00
Molecular weight molecular_weight139060.0 kDa
Excluded volume excluded_volume176390 ų
Envelope volume envelope_volume226860 ų
Hydration-shell volume shell_volume52694 ų
Envelope diameter envelope_diameter131.2
Shell Rg shell_rg42.19
Envelope Rg envelope_rg36.08
Shape Rg shape_rg35.96
Total Rg total_rg36.42
Total atoms total_atoms9773
Residues n_residues1173
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax122.2
Rg (real space) rg_real36.14
Rg uncertainty (real space) rg_real_error0.97
I(0) (real space) i0_real2.7260e+08
I(0) uncertainty (real space) i0_real_error4.2050e+06
Rg (reciprocal space) rg_reciprocal36.12
I(0) (reciprocal space) i0_reciprocal272600000.0000
Solution quality estimate total_estimate0.8743
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.6
Skewness Skewness skewness0.419
Kurtosis Kurtosis kurtosis-0.190
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45950000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.903

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)