5tq3

Design and Synthesis of a pan-JAK kinase inhibitor clinical candidate (PF-06263276) suitable for the treatment of inflammatory diseases of the lungs and skin

Method: X-RAY DIFFRACTION Dmax: 102.0 Å Quality: REASONABLE

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 837–1132 Fragment:UNP residues 837-1132 Mutation:M1073S, F1076S, I1126V Non-standard monomer:Yes (specific site not provided by mmCIF) 7GZ 4-[3-(1H-benzimidazol-2-yl)-1H-indazol-6-yl]-3-ethylphenol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1 M Hepes, pH 7.5, 0.1 M Sodium acetate, 30% PEG3350 Resolution 2.69 Å R-free 0.271
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 837–1132 Fragment:UNP residues 837-1132 Mutation:M1073S, F1076S, I1126V Non-standard monomer:Yes (specific site not provided by mmCIF) 7GZ 4-[3-(1H-benzimidazol-2-yl)-1H-indazol-6-yl]-3-ethylphenol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.1 M Hepes, pH 7.5, 0.1 M Sodium acetate, 30% PEG3350 Resolution 2.69 Å R-free 0.271

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 250 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 9–304; UniProt 837–1132 Author chain B; PDBConstruct 9–304; UniProt 837–1132

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 5tq3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tq3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tq3
Deposition date deposition_date2016-10-23
Structure title titleDesign and Synthesis of a pan-JAK kinase inhibitor clinical candidate (PF-06263276) suitable for the treatment of inflammatory diseases of the lungs and skin
Keywords keywordsKinase, Inflammation, Jak 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_guinier30.72
Radius of gyration Rg (electron density) rg_electron30.26
Forward intensity I(0) i069081300.00
Molecular weight molecular_weight66092.0 kDa
Excluded volume excluded_volume82916 ų
Envelope volume envelope_volume105010 ų
Hydration-shell volume shell_volume30310 ų
Envelope diameter envelope_diameter106.8
Shell Rg shell_rg35.64
Envelope Rg envelope_rg30.41
Shape Rg shape_rg30.25
Total Rg total_rg30.81
Total atoms total_atoms4653
Residues n_residues567
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 dmax102.0
Rg (real space) rg_real30.92
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real6.9080e+07
I(0) uncertainty (real space) i0_real_error1.1080e+06
Rg (reciprocal space) rg_reciprocal30.84
I(0) (reciprocal space) i0_reciprocal69080000.0000
Solution quality estimate total_estimate0.6718
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.4
Skewness Skewness skewness0.471
Kurtosis Kurtosis kurtosis-0.413
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19520000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.837; Smooth: 0.809

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_idd5tq3a_
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_idd5tq3b_
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 (4 domains)

Domain ID domain_id5tq3A01
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_id5tq3A02
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_id5tq3B01
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_id5tq3B02
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)