6tfu

Crystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 14d

Method: X-RAY DIFFRACTION Dmax: 84.5 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 Mutation:T790M, V948R N7K ~{N}-[3-[4-[[1-(phenylmethyl)indazol-5-yl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]phenyl]propanamide × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;32.5 % PEG3350, 100 mM MgSO4, 3 % ethylen glycole 7.2 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) Resolution 2.00 Å R-free 0.233
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 695–1022 Mutation:T790M, V948R N7K ~{N}-[3-[4-[[1-(phenylmethyl)indazol-5-yl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]phenyl]propanamide × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;32.5 % PEG3350, 100 mM MgSO4, 3 % ethylen glycole 7.2 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) Resolution 2.00 Å R-free 0.233

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 6–333; UniProt 695–1022 Author chain B; PDBConstruct 6–333; 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 6tfu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6tfu
Deposition date deposition_date2019-11-14
Structure title titleCrystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 14d
Keywords keywordsHER2, EGFR, covalent Inhibitors, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.22
Radius of gyration Rg (electron density) rg_electron24.41
Forward intensity I(0) i053235900.00
Molecular weight molecular_weight58768.0 kDa
Excluded volume excluded_volume74389 ų
Envelope volume envelope_volume87596 ų
Hydration-shell volume shell_volume29688 ų
Envelope diameter envelope_diameter85.1
Shell Rg shell_rg31.79
Envelope Rg envelope_rg24.50
Shape Rg shape_rg24.41
Total Rg total_rg25.25
Total atoms total_atoms4131
Residues n_residues527
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 dmax84.5
Rg (real space) rg_real25.17
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real5.3240e+07
I(0) uncertainty (real space) i0_real_error7.9080e+05
Rg (reciprocal space) rg_reciprocal25.19
I(0) (reciprocal space) i0_reciprocal53240000.0000
Solution quality estimate total_estimate0.8832
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5
Skewness Skewness skewness0.314
Kurtosis Kurtosis kurtosis-0.329
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21700000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6tfuA01
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_id6tfuA02
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)