5l3a

Fragment-based discovery of 6-arylindazole JAK inhibitors

Method: X-RAY DIFFRACTION Dmax: 68.2 Å Quality: GOOD

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

Tyrosine-protein kinase JAK2

Homo sapiens

UniProt O60674

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 840–1132 Mutation:Y1007F, Y1008F 6DP ~{N}-(1~{H}-indazol-4-yl)methanesulfonamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;2.1M Na Malonate pH 6.0/6.5, 0.1M glycine pH 8.2 Resolution 1.98 Å R-free 0.277

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.

161 other PDB entries and 251 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name JAK2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–295; UniProt 840–1132

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 5l3a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5l3a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5l3a
Deposition date deposition_date2016-04-06
Structure title titleFragment-based discovery of 6-arylindazole JAK inhibitors
Keywords keywordsDouble F mutant, transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.34
Radius of gyration Rg (electron density) rg_electron20.02
Forward intensity I(0) i020337000.00
Molecular weight molecular_weight34153.0 kDa
Excluded volume excluded_volume42769 ų
Envelope volume envelope_volume51276 ų
Hydration-shell volume shell_volume21465 ų
Envelope diameter envelope_diameter68.3
Shell Rg shell_rg26.61
Envelope Rg envelope_rg20.28
Shape Rg shape_rg20.00
Total Rg total_rg20.99
Total atoms total_atoms2403
Residues n_residues290
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 dmax68.2
Rg (real space) rg_real21.28
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real2.0340e+07
I(0) uncertainty (real space) i0_real_error2.4640e+05
Rg (reciprocal space) rg_reciprocal21.29
I(0) (reciprocal space) i0_reciprocal20340000.0000
Solution quality estimate total_estimate0.8913
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.1
Skewness Skewness skewness0.295
Kurtosis Kurtosis kurtosis-0.306
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4810000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.933

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5l3aa_
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

CATH v4.4 (2 domains)

Domain ID domain_id5l3aA01
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_id5l3aA02
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)