MolNFT v1 · #62694 · protein
Targeted polypharmacology: crystal structure of the C-src kinase domain in complex with PP494, a multitargeted kinase inhibitor
3EN5 · Proto-oncogene tyrosine-protein kinase src: “Targeted polypharmacology: crystal structure of the C-src kinase domain in complex with PP494, a…”. X-ray diffraction, 1 ligand (KS4), 5 pockets (best druggability 0.74). MolNFT v1 #62694…
- PDB
- 3EN5
- Type
- protein
- Length
- 499 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
- KS4
- Pockets
- 5 · best druggability 0.74
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 2.7.10.2) | protein | 238 | 44% helix, 17% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 261 | 43% helix, 16% strand | P00523 |
Ligands and binding sites
- KS4 · 1-cyclobutyl-3-(3,4-dimethoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.74 | 0.78 | 86 | KS4 |
| 2 | 415 | 0.62 | 0.77 | 45 | empty |
| 3 | 352 | 0.59 | 0.76 | 30 | KS4 |
| 4 | 53 | 0.31 | 0.76 | 15 | empty |
| 5 | 63 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 457 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3EN5 · 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 3EN5 · PDBe 3EN5 · UniProt P00523
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