6tpf

Fragment-based discovery of pyrazolopyridones as JAK1 inhibitors with excellent subtype selectivity

Method: X-RAY DIFFRACTION Dmax: 99.2 Å Quality: REASONABLE

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

Tyrosine-protein kinase JAK1

OrganismNot specified

UniProt P23458

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 864–1154 Fragment:KINASE DOMAIN Non-standard monomer:Yes (specific site not provided by mmCIF) NTQ (1~{S})-2,2-bis(fluoranyl)-~{N}-[4-(3-methyl-6-oxidanylidene-2,7-dihydropyrazolo[3,4-b]pyridin-4-yl)cyclohexyl]cyclopropane-1-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;277 K;NULL Resolution 2.31 Å R-free 0.327
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 864–1154 Fragment:KINASE DOMAIN Non-standard monomer:Yes (specific site not provided by mmCIF) NTQ (1~{S})-2,2-bis(fluoranyl)-~{N}-[4-(3-methyl-6-oxidanylidene-2,7-dihydropyrazolo[3,4-b]pyridin-4-yl)cyclohexyl]cyclopropane-1-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;277 K;NULL Resolution 2.31 Å R-free 0.327

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.

49 other PDB entries and 84 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name JAK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–291; UniProt 864–1154 Author chain B; PDBConstruct 1–291; UniProt 864–1154

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 6tpf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6tpf
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6tpf
Deposition date deposition_date2019-12-13
Structure title titleFragment-based discovery of pyrazolopyridones as JAK1 inhibitors with excellent subtype selectivity
Keywords keywordsJANUS KINASE, INHIBITOR, COMPLEX, PROTEROS BIOSTRUCTURES GMBH, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.51
Radius of gyration Rg (electron density) rg_electron29.97
Forward intensity I(0) i069913400.00
Molecular weight molecular_weight66237.0 kDa
Excluded volume excluded_volume83095 ų
Envelope volume envelope_volume106120 ų
Hydration-shell volume shell_volume30243 ų
Envelope diameter envelope_diameter106.2
Shell Rg shell_rg36.27
Envelope Rg envelope_rg29.96
Shape Rg shape_rg29.99
Total Rg total_rg30.50
Total atoms total_atoms4650
Residues n_residues562
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 dmax99.2
Rg (real space) rg_real30.61
Rg uncertainty (real space) rg_real_error0.77
I(0) (real space) i0_real6.9910e+07
I(0) uncertainty (real space) i0_real_error1.0850e+06
Rg (reciprocal space) rg_reciprocal30.57
I(0) (reciprocal space) i0_reciprocal69910000.0000
Solution quality estimate total_estimate0.6920
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.344
Kurtosis Kurtosis kurtosis-0.676
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26140000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.880; Smooth: 0.954

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)