MolNFT v1 · #151381 · protein
Crystal structure of spleen tyrosine kinase (syk) in complex with a 2- (PHENOXYMETHYL)PYRIDINE inhibitor
6HM7 · Tyrosine-protein kinase syk: “Crystal structure of spleen tyrosine kinase (syk) in complex with a 2- (PHENOXYMETHYL)PYRIDINE inhibitor”. X-ray diffraction, 2 ligands (GDH, BR), 3 pockets (best druggability 0.57). MolNFT v1 #151381…
- PDB
- 6HM7
- Type
- protein
- Length
- 268 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase syk
- EC
- 2.7.10.2
- UniProt
- P43405
- Ligands
- GDH, BR
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 268 | 41% helix, 21% strand | P43405 |
Ligands and binding sites
- GDH · 7-[2-methoxy-6-[(4-methylpyridin-2-yl)methoxy]phenyl]-2,3,4,5-tetrahydro-1~{H}-3-benzazepine · ligand · chains A
- BR · Bromide ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.57 | 0.79 | 26 | GDH |
| 2 | 73 | 0.36 | 0.77 | 14 | empty |
| 3 | 62 | 0.30 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6HM7 · Crystal structure of spleen tyrosine kinase (syk) in complex with a… · 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 6HM7 · PDBe 6HM7 · UniProt P43405
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