Research workbench
Crystal structure of src kinase domain in complex with CGP77675
Analyse Crystal structure of src kinase domain in complex with CGP77675 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YOL
- Type
- protein
- Length
- 509 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
- S03
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.1.112) | protein | 256 | 44% helix, 17% strand | P12931 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.1.112) | protein | 253 | 43% helix, 16% strand | P12931 |
Ligands and binding sites
- S03 · 1-{4-[4-amino-5-(3-methoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl]benzyl}piperidin-4-ol · 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 | 740 | 0.71 | 0.78 | 74 | S03 |
| 2 | 337 | 0.66 | 0.81 | 41 | S03 |
| 3 | 385 | 0.62 | 0.78 | 46 | empty |
| 4 | 93 | 0.33 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 390 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1YOL · Crystal structure of Src kinase domain in complex with CGP77675 · 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 1YOL · PDBe 1YOL · UniProt P12931
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