6rse

Structure based optimization of JAK1-ATP binding pocket Inhibitors in the aminopyrazole class

Method: X-RAY DIFFRACTION Dmax: 98.6 Å Quality: GOOD

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

Tyrosine-protein kinase JAK1

Homo sapiens

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 854–1154 Non-standard monomer:Yes (specific site not provided by mmCIF) KHH methyl ~{N}-[4-aminocarbonyl-1-[(3~{R},4~{R})-4-(cyanomethyl)-1-[(4-ethenyl-2-fluoranyl-5-oxidanyl-phenyl)methyl]-3-fluoranyl-piperidin-4-yl]pyrazol-3-yl]carbamate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.6;277 K;0.1M MES. 25-35% PEG6000 Resolution 1.80 Å R-free 0.303
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 854–1154 Non-standard monomer:Yes (specific site not provided by mmCIF) KHH methyl ~{N}-[4-aminocarbonyl-1-[(3~{R},4~{R})-4-(cyanomethyl)-1-[(4-ethenyl-2-fluoranyl-5-oxidanyl-phenyl)methyl]-3-fluoranyl-piperidin-4-yl]pyrazol-3-yl]carbamate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.6;277 K;0.1M MES. 25-35% PEG6000 Resolution 1.80 Å R-free 0.303

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 2–302; UniProt 854–1154 Author chain B; PDBConstruct 2–302; UniProt 854–1154

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 6rse

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6rse
Deposition date deposition_date2019-05-21
Structure title titleStructure based optimization of JAK1-ATP binding pocket Inhibitors in the aminopyrazole class
Keywords keywordsInhibitor, Complex, 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_electron30.16
Forward intensity I(0) i070791000.00
Molecular weight molecular_weight66673.0 kDa
Excluded volume excluded_volume83648 ų
Envelope volume envelope_volume104410 ų
Hydration-shell volume shell_volume29718 ų
Envelope diameter envelope_diameter102.2
Shell Rg shell_rg36.21
Envelope Rg envelope_rg30.02
Shape Rg shape_rg30.18
Total Rg total_rg30.69
Total atoms total_atoms4681
Residues n_residues563
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 dmax98.6
Rg (real space) rg_real30.73
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real7.0790e+07
I(0) uncertainty (real space) i0_real_error9.9540e+05
Rg (reciprocal space) rg_reciprocal30.68
I(0) (reciprocal space) i0_reciprocal70790000.0000
Solution quality estimate total_estimate0.8753
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.4
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.686
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23630000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.873; Smooth: 0.901

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6rsea_
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.144.1.0 — automated matches
Domain ID domain_idd6rseb_
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.144.1.0 — automated matches

8. Citations (1)

9. Files and Curves (10)