5tq7

Design and Synthesis of a pan-JAK Kinase Inhibitor Clinical Candidate (PF-06263276) Suitable for Inhaled and Topical Delivery for the Treatment of Inflammatory Diseases of the Lungs and Skin

Method: X-RAY DIFFRACTION Dmax: 113.3 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 837–1132 Fragment:UNP residues 837-1132 Mutation:M1073S, F1076T, I1126V Non-standard monomer:Yes (specific site not provided by mmCIF) 7GT {(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}[(3R)-3-(phenylsulfonyl)pyrrolidin-1-yl]methanone × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;0.1 M Hepes, pH 7.5, 100 mM sodium acetate, 30% PEG3350 Resolution 2.10 Å R-free 0.286
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, F1076T, I1126V Non-standard monomer:Yes (specific site not provided by mmCIF) 7GT {(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}[(3R)-3-(phenylsulfonyl)pyrrolidin-1-yl]methanone × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;0.1 M Hepes, pH 7.5, 100 mM sodium acetate, 30% PEG3350 Resolution 2.10 Å R-free 0.286

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 5tq7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tq7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tq7
Deposition date deposition_date2016-10-23
Structure title titleDesign and Synthesis of a pan-JAK Kinase Inhibitor Clinical Candidate (PF-06263276) Suitable for Inhaled and Topical Delivery 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_guinier32.14
Radius of gyration Rg (electron density) rg_electron32.10
Forward intensity I(0) i065144100.00
Molecular weight molecular_weight64606.0 kDa
Excluded volume excluded_volume81159 ų
Envelope volume envelope_volume104740 ų
Hydration-shell volume shell_volume29135 ų
Envelope diameter envelope_diameter118.6
Shell Rg shell_rg36.06
Envelope Rg envelope_rg32.23
Shape Rg shape_rg32.11
Total Rg total_rg32.43
Total atoms total_atoms4543
Residues n_residues544
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 dmax113.3
Rg (real space) rg_real32.55
Rg uncertainty (real space) rg_real_error1.33
I(0) (real space) i0_real6.5140e+07
I(0) uncertainty (real space) i0_real_error1.1120e+06
Rg (reciprocal space) rg_reciprocal32.38
I(0) (reciprocal space) i0_reciprocal65130000.0000
Solution quality estimate total_estimate0.7982
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.7
Skewness Skewness skewness0.571
Kurtosis Kurtosis kurtosis-0.316
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19400000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.617; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.621; Smooth: 0.905

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_idd5tq7a_
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_idd5tq7b_
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_id5tq7A01
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_id5tq7A02
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_id5tq7B01
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_id5tq7B02
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)