› 5c27

X-ray diffraction
2.15Å resolution

Crystal structure of SYK in complex with compound 2

Released:
DOI: 10.2210/pdb5c27/pdb
PDB entry 5c27 coloured by chain, front view.
PDB entry 5c27 coloured by chain, side view.
PDB entry 5c27 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Imidazotriazines: Spleen Tyrosine Kinase (Syk) Inhibitors Identified by Free-Energy Perturbation (FEP).
Lovering F, Aevazelis C, Chang J, Dehnhardt C, Fitz L, Han S, Janz K, Lee J, Kaila N, McDonald J, Moore W, Moretto A, Papaioannou N, Richard D, Ryan MS, Wan ZK, Thorarensen A
ChemMedChem 11 217-33 (2016)
PMID: 26381330

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155060 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Tyrosine-protein kinase SYK Chain: A
Molecule details ›
Chain: A
Length: 299 amino acids
Theoretical weight: 35.04 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P43405 (Residues: 343-635; Coverage: 46%)
Gene name: SYK
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:
GLU-VAL-TYR-GLU-SER Chain: D
Molecule details ›
Chain: D
Length: 5 amino acids
Theoretical weight: 626 Da
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda

Ligands and Environments

2 bound ligands:
Ligand 50J 1 x 50J
Ligand GOL 1 x GOL
1 modified residue:
Ligand PTR 2 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 39.879Å b: 84.875Å c: 89.592Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.177 0.225
Expression system: Spodoptera frugiperda

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Citations

4 review citations

Accelerating drug discovery through tight integration of expert molecular design and predictive scoring.
Abel et al. (2017)
3 more