MolNFT v1 · #39528 · protein
Crystal structure of src kinase domain in complex with covalent inhibitor PD168393
2HWP · Proto-oncogene tyrosine-protein kinase src: “Crystal structure of src kinase domain in complex with covalent inhibitor PD168393”. X-ray diffraction, 1 ligand (DJK), 6 pockets (best druggability 0.59). MolNFT v1 #39528 on GenesisL1…
- PDB
- 2HWP
- Type
- protein
- Length
- 484 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
- DJK
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 245 | 42% helix, 13% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 239 | 43% helix, 17% strand | P00523 |
Ligands and binding sites
- DJK · N-[4-(3-bromo-phenylamino)-quinazolin-6-yl]-acrylamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.59 | 0.78 | 38 | DJK |
| 2 | 313 | 0.55 | 0.76 | 30 | empty |
| 3 | 293 | 0.51 | 0.74 | 36 | DJK |
| 4 | 81 | 0.41 | 0.78 | 12 | empty |
| 5 | 61 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 338 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2HWP · Crystal structure of Src kinase domain in complex with covalent inhibitor PD168393 · 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 2HWP · PDBe 2HWP · UniProt P00523
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