6wa2

Crystal structure of EGFR(T790M/V948R) in complex with LN3753

Method: X-RAY DIFFRACTION Dmax: 104.6 Å Quality: REASONABLE

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 695–1022 Chain D; UniProt 695–1022 Not recorded TOV N-(3-{5-[2-(acetylamino)pyridin-4-yl]-2-(methylsulfanyl)-1H-imidazol-4-yl}phenyl)-2-fluoro-5-hydroxybenzamide × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;25% PEG-3350 0.1 M BisTris Resolution 2.40 Å R-free 0.258
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 695–1022 Chain C; UniProt 695–1022 Not recorded TOV N-(3-{5-[2-(acetylamino)pyridin-4-yl]-2-(methylsulfanyl)-1H-imidazol-4-yl}phenyl)-2-fluoro-5-hydroxybenzamide × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;25% PEG-3350 0.1 M BisTris Resolution 2.40 Å R-free 0.258

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 564 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 1–328; UniProt 695–1022 Author chain B; PDBConstruct 1–328; UniProt 695–1022 Author chain C; PDBConstruct 1–328; UniProt 695–1022 Author chain D; PDBConstruct 1–328; 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 6wa2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6wa2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6wa2
Deposition date deposition_date2020-03-24
Structure title titleCrystal structure of EGFR(T790M/V948R) in complex with LN3753
Keywords keywordsDrug discovery, Cancer, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.25
Radius of gyration Rg (electron density) rg_electron33.42
Forward intensity I(0) i0299154000.00
Molecular weight molecular_weight142800.0 kDa
Excluded volume excluded_volume180310 ų
Envelope volume envelope_volume227250 ų
Hydration-shell volume shell_volume54685 ų
Envelope diameter envelope_diameter110.7
Shell Rg shell_rg41.83
Envelope Rg envelope_rg33.07
Shape Rg shape_rg33.41
Total Rg total_rg34.09
Total atoms total_atoms10017
Residues n_residues1230
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 dmax104.6
Rg (real space) rg_real34.09
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real2.9920e+08
I(0) uncertainty (real space) i0_real_error4.6710e+06
Rg (reciprocal space) rg_reciprocal34.19
I(0) (reciprocal space) i0_reciprocal299200000.0000
Solution quality estimate total_estimate0.6983
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.2
Skewness Skewness skewness0.156
Kurtosis Kurtosis kurtosis-0.482
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha87980000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 0.122; Positv: 1.000; Valcen: 0.984; Smooth: 0.878

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6wa2a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd6wa2b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd6wa2c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd6wa2d_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (8 domains)

Domain ID domain_id6wa2A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6wa2A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id6wa2B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6wa2B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id6wa2C01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6wa2C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id6wa2D01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6wa2D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)