MolNFT v1 · #122977 · protein
Src kinase in complex with a sulfonamide inhibitor
5J5S · Proto-oncogene tyrosine-protein kinase src: “Src kinase in complex with a sulfonamide inhibitor”. X-ray diffraction, 1 ligand (6G3), 3 pockets (best druggability 0.75). MolNFT v1 #122977 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5J5S
- Type
- protein
- Length
- 516 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
- 6G3
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 258 | 43% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 258 | 43% helix, 16% strand | P00523 |
Ligands and binding sites
- 6G3 · N-{4-[8-amino-3-(propan-2-yl)imidazo[1,5-a]pyrazin-1-yl]naphthalen-1-yl}-N'-[3-(trifluoromethyl)phenyl]urea · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.75 | 0.79 | 84 | 6G3 |
| 2 | 417 | 0.68 | 0.80 | 48 | 6G3 |
| 3 | 394 | 0.59 | 0.76 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 338 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5J5S · Src kinase in complex with a sulfonamide inhibitor · 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 5J5S · PDBe 5J5S · UniProt P00523
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