Research workbench
Crystal structure of C-src in complex with pyrazolopyrimidine 5
Analyse Crystal structure of C-src in complex with pyrazolopyrimidine 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EL8
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- PD5
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 263 | 38% helix, 18% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 259 | 39% helix, 17% strand | P00523 |
Ligands and binding sites
- PD5 · 1-{4-[4-amino-1-(1-methylethyl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]phenyl}-3-[3-(trifluoromethyl)phenyl]urea · ligand · chains A
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 | 363 | 0.73 | 0.85 | 48 | PD5 |
| 2 | 747 | 0.71 | 0.77 | 69 | empty |
| 3 | 337 | 0.57 | 0.76 | 41 | empty |
| 4 | 52 | 0.29 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 420 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3EL8 · Crystal structure of c-Src in complex with pyrazolopyrimidine 5 · 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 P00523
- Elsewhere: RCSB PDB 3EL8 · PDBe 3EL8 · UniProt P00523
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