MolNFT v1 · #39527 · protein
Crystal structure of src kinase domain in complex with covalent inhibitor
2HWO · Proto-oncogene tyrosine-protein kinase src: “Crystal structure of src kinase domain in complex with covalent inhibitor”. X-ray diffraction, 1 ligand (RBS), 3 pockets (best druggability 0.74). MolNFT v1 #39527 on GenesisL1: 3D…
- PDB
- 2HWO
- 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
- RBS
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 251 | 40% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 242 | 41% helix, 17% strand | P00523 |
Ligands and binding sites
- RBS · N-(4-phenylamino-quinazolin-6-yl)-acrylamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.74 | 0.77 | 110 | RBS, GOL |
| 2 | 262 | 0.57 | 0.78 | 32 | RBS |
| 3 | 55 | 0.32 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 412 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2HWO · Crystal structure of Src kinase domain in complex with covalent 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 2HWO · PDBe 2HWO · UniProt P00523
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