MolNFT v1 · #114854 · protein
Crystal structure of syk in complex with compound 1
5C26 · Tyrosine-protein kinase syk: “Crystal structure of syk in complex with compound 1”. X-ray diffraction, 1 ligand (50H), 2 pockets (best druggability 0.68). MolNFT v1 #114854 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5C26
- Type
- protein
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase syk; Glu-val-ptr-glu-ser-pro
- EC
- 2.7.10.2
- UniProt
- P43405
- Ligands
- 50H
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 274 | 40% helix, 23% strand | P43405 |
| B | Glu-val-ptr-glu-ser-pro | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- 50H · 3-{8-[(3,4-dimethoxyphenyl)amino]imidazo[1,2-a]pyrazin-6-yl}benzamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.68 | 0.78 | 49 | 50H |
| 2 | 50 | 0.28 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 5C26 · Crystal structure of SYK in complex with compound 1 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P43405
- Elsewhere: RCSB PDB 5C26 · PDBe 5C26 · UniProt P43405
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