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Crystal structure of pyrazolo pyrimidine derivative bound to the kinase domain of human lck, (auto-phosphorylated on TYR394)
Analyse Crystal structure of pyrazolo pyrimidine derivative bound to the kinase domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AD6
- 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
- KSC, SO4
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% 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, 19% strand | P06239 |
Ligands and binding sites
- KSC · 7-[(cyclopropylmethyl)amino]-2-[(4-methoxyphenyl)amino]-5-methylpyrazolo[1,5-a]pyrimidine-3-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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 | 354 | 0.61 | 0.77 | 41 | KSC |
| 2 | 62 | 0.38 | 0.79 | 18 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3AD6 · Crystal structure of Pyrazolo pyrimidine derivative bound to the kinase domain of human… · 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 3AD6 · PDBe 3AD6 · UniProt P06239
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