MolNFT v1 · #134505 · protein
Crystal structure of syk catalytic domain in complex with a FURO[3,2- D]PYRIMIDINE
5T68 · Tyrosine-protein kinase syk: “Crystal structure of syk catalytic domain in complex with a FURO[3,2- D]PYRIMIDINE”. X-ray diffraction, 1 ligand (77V), 4 pockets (best druggability 0.63). MolNFT v1 #134505 on GenesisL1: 3D structure…
- PDB
- 5T68
- Type
- protein
- Length
- 530 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
- 77V
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 266 | 38% helix, 23% strand | P43405 |
| B | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 264 | 38% helix, 24% strand | P43405 |
Ligands and binding sites
- 77V · N~4~-cyclopropyl-N~2~-(3-methyl-1H-indazol-6-yl)furo[3, 2-d]pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.63 | 0.81 | 32 | 77V |
| 2 | 272 | 0.63 | 0.81 | 34 | 77V |
| 3 | 185 | 0.53 | 0.78 | 30 | empty |
| 4 | 50 | 0.31 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 690 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5T68 · Crystal structure of Syk catalytic domain in complex with a furo[3,2-d]pyrimidine · 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 5T68 · PDBe 5T68 · UniProt P43405
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