Research workbench
Crystal structure of src kinase domain in complex with purvalanol a
Analyse Crystal structure of src kinase domain in complex with purvalanol a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YOM
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.1.112
- UniProt
- P12931
- Ligands
- P01
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.1.112) | protein | 260 | 37% helix, 13% strand | P12931 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.1.112) | protein | 261 | 40% helix, 13% strand | P12931 |
Ligands and binding sites
- P01 · 2-({6-[(3-chlorophenyl)amino]-9-isopropyl-9H-purin-2-yl}amino)-3-methylbutan-1-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.76 | 0.79 | 87 | P01 |
| 2 | 449 | 0.66 | 0.78 | 44 | P01 |
| 3 | 65 | 0.33 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 400 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1YOM · Crystal structure of Src kinase domain in complex with Purvalanol A · 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 P12931
- Elsewhere: RCSB PDB 1YOM · PDBe 1YOM · UniProt P12931
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