MolNFT v1 · #49360 · protein
Crystal structure of src kinase domain with covalent inhibitor RL3
2QLQ · Proto-oncogene tyrosine-protein kinase src: “Crystal structure of src kinase domain with covalent inhibitor RL3”. X-ray diffraction, 1 ligand (SR2), 4 pockets (best druggability 0.69). MolNFT v1 #49360 on GenesisL1: 3D structure…
- PDB
- 2QLQ
- Type
- protein
- Length
- 493 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
- SR2
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 245 | 41% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 248 | 38% helix, 18% strand | P00523 |
Ligands and binding sites
- SR2 · (2E)-N-{4-[(3-bromophenyl)amino]quinazolin-6-yl}-4-(dimethylamino)but-2-enamide · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.69 | 0.77 | 71 | SR2 |
| 2 | 363 | 0.60 | 0.77 | 45 | empty |
| 3 | 340 | 0.59 | 0.77 | 39 | SR2 |
| 4 | 77 | 0.30 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 408 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 2QLQ · Crystal structure of SRC kinase domain with covalent inhibitor RL3 · the same entry in another collection · chain B against B, 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 2QLQ · PDBe 2QLQ · UniProt P00523
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