MolNFT v1 · #109891 · protein
Crystal structure of an inhibitor-bound syk
4XG3 · Tyrosine-protein kinase syk: “Crystal structure of an inhibitor-bound syk”. X-ray diffraction, 1 ligand (X3G), 6 pockets (best druggability 0.68). MolNFT v1 #109891 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XG3
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- 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
- X3G
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 262 | 40% helix, 23% strand | P43405 |
| B | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 267 | 39% helix, 23% strand | P43405 |
Ligands and binding sites
- X3G · 4-{[5-fluoro-4-(3-{[(3R)-3-hydroxypyrrolidin-1-yl]methyl}-4-methyl-1H-pyrrol-1-yl)pyrimidin-2-yl]amino}-2,6-dimethylphenyl methanesulfonate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.68 | 0.78 | 57 | X3G |
| 2 | 189 | 0.57 | 0.80 | 24 | X3G |
| 3 | 238 | 0.51 | 0.75 | 36 | empty |
| 4 | 89 | 0.33 | 0.73 | 17 | empty |
| 5 | 60 | 0.33 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 569 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4XG3 · Crystal structure of an inhibitor-bound Syk · 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 4XG3 · PDBe 4XG3 · UniProt P43405
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