Research workbench
X-ray crystal structure of 2-aminopyrimidine carbamate 43 bound to lck
Analyse X-ray crystal structure of 2-aminopyrimidine carbamate 43 bound to lck in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OFU
- Type
- protein
- Length
- 273 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase lck
- EC
- 2.7.10.2
- UniProt
- P06239
- Ligands
- 1N9, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase lck (EC 2.7.10.2) | protein | 273 | 38% helix, 20% strand | P06239 |
Ligands and binding sites
- 1N9 · 2,6-dimethylphenyl 2-(3,5-dimethoxy-4-(3-(4-methylpiperazin-1-yl)propoxy)phenylamino)pyrimidin- 4-yl(2,4-dimethoxyphenyl)carbamate · ligand · chains A
- SO4 · Sulfate ion · ion · 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 | 362 | 0.63 | 0.78 | 34 | 1N9 |
| 2 | 50 | 0.35 | 0.79 | 18 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 2OFU · x-ray crystal structure of 2-aminopyrimidine carbamate 43 bound to Lck · the same entry in another collection · chain A against A, TM-score 1.00
- P06239 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase lck (P06239) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P06239
- Elsewhere: RCSB PDB 2OFU · PDBe 2OFU · UniProt P06239
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