MolNFT v1 · #59458 · protein
X-ray co-crystal structure of 2-amino-6-PHENYLPYRIMIDO[5', 4':5,6]PYRIMIDO[1,2-A]BENZIMIDAZOL-5(6H)-one 25 bound to lck
3BYO · Proto-oncogene tyrosine-protein kinase lck: “X-ray co-crystal structure of 2-amino-6-PHENYLPYRIMIDO[5', 4':5,6]PYRIMIDO[1,2-A]BENZIMIDAZOL-5(6H)-one 25…”. X-ray diffraction, 2 ligands (AM9, SO4), 1 pocket (best druggability 0.60).…
- PDB
- 3BYO
- Type
- protein
- Length
- 271 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
- AM9, SO4
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase lck (EC 2.7.10.2) | protein | 271 | 39% helix, 20% strand | P06239 |
Ligands and binding sites
- AM9 · 6-(2,6-dimethylphenyl)-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-one · 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.60 | 0.78 | 34 | AM9 |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3BYO · X-Ray co-crystal structure of 2-amino-6-phenylpyrimido[5',4':5,6]pyrimido[1,2-a]benzimidaz… · 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 P06239
- Elsewhere: RCSB PDB 3BYO · PDBe 3BYO · UniProt P06239
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