5z0s

Crystal structure of FGFR1 kinase domain in complex with a novel inhibitor

Method: X-RAY DIFFRACTION Dmax: 92.5 Å Quality: EXCELLENT

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 Fragment:UNP residues 458-765 Mutation:C488A, C584S 960 1-[(6-chloroimidazo[1,2-b]pyridazin-3-yl)sulfonyl]-6-(1-methyl-1H-pyrazol-4-yl)-1H-pyrazolo[4,3-b]pyridine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;0.1M Bis-Tris pH 6.5, 0.3M (NH4)2SO4, 15-20% PEG10000, 5% EG Resolution 2.45 Å R-free 0.275
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 458–765 Fragment:UNP residues 458-765 Mutation:C488A, C584S 960 1-[(6-chloroimidazo[1,2-b]pyridazin-3-yl)sulfonyl]-6-(1-methyl-1H-pyrazol-4-yl)-1H-pyrazolo[4,3-b]pyridine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;0.1M Bis-Tris pH 6.5, 0.3M (NH4)2SO4, 15-20% PEG10000, 5% EG Resolution 2.45 Å R-free 0.275

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 1–308; UniProt 458–765 Author chain B; PDBConstruct 1–308; 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 5z0s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5z0s
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5z0s
Deposition date deposition_date2017-12-20
Structure title titleCrystal structure of FGFR1 kinase domain in complex with a novel inhibitor
Keywords keywordsFGFR1 inhibitor, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.60
Radius of gyration Rg (electron density) rg_electron28.97
Forward intensity I(0) i065766100.00
Molecular weight molecular_weight64029.0 kDa
Excluded volume excluded_volume80440 ų
Envelope volume envelope_volume102830 ų
Hydration-shell volume shell_volume29905 ų
Envelope diameter envelope_diameter98.6
Shell Rg shell_rg35.70
Envelope Rg envelope_rg28.69
Shape Rg shape_rg28.98
Total Rg total_rg29.63
Total atoms total_atoms4491
Residues n_residues566
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 dmax92.5
Rg (real space) rg_real29.61
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real6.5770e+07
I(0) uncertainty (real space) i0_real_error9.2470e+05
Rg (reciprocal space) rg_reciprocal29.61
I(0) (reciprocal space) i0_reciprocal65770000.0000
Solution quality estimate total_estimate0.9023
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.4
Skewness Skewness skewness0.262
Kurtosis Kurtosis kurtosis-0.679
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42180000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.944

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5z0sa_
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_idd5z0sb_
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_id5z0sA01
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_id5z0sA02
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_id5z0sB01
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_id5z0sB02
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)