MolNFT v1 · #110931 · protein
Type II dasatinib analog crystallized with C-src kinase
4YBJ · Proto-oncogene tyrosine-protein kinase src: “Type II dasatinib analog crystallized with C-src kinase”. X-ray diffraction, 1 ligand (4A9), 5 pockets (best druggability 0.75). MolNFT v1 #110931 on GenesisL1: 3D structure, binding…
- PDB
- 4YBJ
- Type
- protein
- Length
- 508 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
- 4A9
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 255 | 44% helix, 17% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 253 | 40% helix, 14% strand | P00523 |
Ligands and binding sites
- 4A9 · 2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-N-(3-{[3-(trifluoromethyl)benzoyl]amino}phenyl)-1,3-thiazole-5-carboxamide · 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 | 709 | 0.75 | 0.81 | 67 | 4A9 |
| 2 | 356 | 0.72 | 0.84 | 50 | 4A9 |
| 3 | 273 | 0.55 | 0.77 | 30 | empty |
| 4 | 137 | 0.37 | 0.73 | 25 | empty |
| 5 | 64 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 358 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4YBJ · Type II Dasatinib Analog Crystallized with c-Src Kinase · 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 4YBJ · PDBe 4YBJ · UniProt P00523
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.