MolNFT v1 · #76455 · protein
Crystal structure of the L317I mutant of the C-src tyrosine kinase domain complexed with pyrazolopyrimidine 5
3QLF · Proto-oncogene tyrosine-protein kinase src: “Crystal structure of the L317I mutant of the C-src tyrosine kinase domain complexed with pyrazolopyrimidine 5”. X-ray diffraction, 1 ligand (PD5), 5 pockets (best druggability 0.71).…
- PDB
- 3QLF
- Type
- protein
- Length
- 507 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
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 249 | 40% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 258 | 42% 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 · 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 | 721 | 0.71 | 0.78 | 69 | PD5 |
| 2 | 396 | 0.68 | 0.80 | 45 | PD5 |
| 3 | 344 | 0.60 | 0.77 | 40 | empty |
| 4 | 104 | 0.33 | 0.73 | 24 | empty |
| 5 | 52 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 385 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3QLF · Crystal structure of the L317I mutant of the C-src tyrosine kinase domain complexed 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 3QLF · PDBe 3QLF · UniProt P00523
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