6p69

Crystal structure of FGFR1-Y563C (FGFR4 surrogate) covalently bound to compound 11.

Method: X-RAY DIFFRACTION Dmax: 107.9 Å Quality: GOOD

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

Fibroblast growth factor receptor 1

Homo sapiens

UniProt P11362

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 458–765 Mutation:C488A, Y563C SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2 O21 N-{2-[(6-{[(2,6-dichloro-3,5-dimethoxyphenyl)carbamoyl][3-(4-methylpiperazin-1-yl)propyl]amino}pyrimidin-4-yl)amino]phenyl}prop-2-enamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;1:1 mix of protein + reservoir Protein at ~15 mg/mL formulated in: 20mM Tris pH 8, 20mM NaCl, 2mM TCEP Reservoir: 14-18% PEG 10K 0.3 M (NH4)2SO4 0.1 M MES pH 6.5 5% ethylene glycol Resolution 2.20 Å R-free 0.245
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 458–765 Mutation:C488A, Y563C SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 O21 N-{2-[(6-{[(2,6-dichloro-3,5-dimethoxyphenyl)carbamoyl][3-(4-methylpiperazin-1-yl)propyl]amino}pyrimidin-4-yl)amino]phenyl}prop-2-enamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;1:1 mix of protein + reservoir Protein at ~15 mg/mL formulated in: 20mM Tris pH 8, 20mM NaCl, 2mM TCEP Reservoir: 14-18% PEG 10K 0.3 M (NH4)2SO4 0.1 M MES pH 6.5 5% ethylene glycol Resolution 2.20 Å R-free 0.245

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.

77 other PDB entries and 149 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FGFR1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–309; UniProt 458–765 Author chain B; PDBConstruct 2–309; UniProt 458–765

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 6p69

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6p69
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6p69
Deposition date deposition_date2019-06-03
Structure title titleCrystal structure of FGFR1-Y563C (FGFR4 surrogate) covalently bound to compound 11.
Keywords keywordsFGFR, Inhibitor Complex, Covalent inhibitor, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.61
Radius of gyration Rg (electron density) rg_electron30.61
Forward intensity I(0) i071740000.00
Molecular weight molecular_weight66826.0 kDa
Excluded volume excluded_volume83713 ų
Envelope volume envelope_volume107280 ų
Hydration-shell volume shell_volume31206 ų
Envelope diameter envelope_diameter112.5
Shell Rg shell_rg35.02
Envelope Rg envelope_rg30.91
Shape Rg shape_rg30.59
Total Rg total_rg31.06
Total atoms total_atoms4677
Residues n_residues574
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 dmax107.9
Rg (real space) rg_real30.96
Rg uncertainty (real space) rg_real_error1.05
I(0) (real space) i0_real7.1740e+07
I(0) uncertainty (real space) i0_real_error1.1400e+06
Rg (reciprocal space) rg_reciprocal30.81
I(0) (reciprocal space) i0_reciprocal71730000.0000
Solution quality estimate total_estimate0.7982
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.0
Skewness Skewness skewness0.641
Kurtosis Kurtosis kurtosis-0.062
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44640000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.638; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.650; Smooth: 0.809

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6p69a_
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_idd6p69b_
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 (4 domains)

Domain ID domain_id6p69A01
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_id6p69A02
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_id6p69B01
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_id6p69B02
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)