MolNFT v1 · #62695 · protein
Targeted polypharmacology: crystal structure of the C-src kinase domain in complex with PP102, a multitargeted kinase inhibitor
3EN6 · Proto-oncogene tyrosine-protein kinase src: “Targeted polypharmacology: crystal structure of the C-src kinase domain in complex with PP102, a…”. X-ray diffraction, 1 ligand (KS5), 5 pockets (best druggability 0.62). MolNFT v1 #62695…
- PDB
- 3EN6
- Type
- protein
- Length
- 475 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
- KS5
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 236 | 42% helix, 17% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 239 | 43% helix, 17% strand | P00523 |
Ligands and binding sites
- KS5 · 1-(1-methylethyl)-3-quinolin-6-yl-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.62 | 0.77 | 64 | KS5 |
| 2 | 350 | 0.58 | 0.76 | 41 | empty |
| 3 | 139 | 0.41 | 0.74 | 21 | empty |
| 4 | 90 | 0.40 | 0.77 | 12 | empty |
| 5 | 56 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 341 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3EN6 · Targeted polypharmacology: crystal structure of the c-Src kinase domain in complex with… · 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 3EN6 · PDBe 3EN6 · UniProt P00523
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