MolNFT v1 · #32007 · protein
Src kinase in complex with inhibitor AP23451
2BDF · Proto-oncogene tyrosine-protein kinase src: “Src kinase in complex with inhibitor AP23451”. X-ray diffraction, 1 ligand (24A), 6 pockets (best druggability 0.64). MolNFT v1 #32007 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2BDF
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.1.112
- UniProt
- P12931
- Ligands
- 24A
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.1.112) | protein | 261 | 41% helix, 19% strand | P12931 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.1.112) | protein | 265 | 43% helix, 18% strand | P12931 |
Ligands and binding sites
- 24A · {[(4-{[2-(4-aminocyclohexyl)-9-ethyl-9H-purin-6-yl]amino}phenyl)(hydroxy)phosphoryl]methyl}phosphonic acid · 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 | 364 | 0.64 | 0.79 | 38 | 24A |
| 2 | 334 | 0.64 | 0.80 | 39 | 24A |
| 3 | 282 | 0.59 | 0.78 | 30 | empty |
| 4 | 64 | 0.38 | 0.79 | 16 | empty |
| 5 | 71 | 0.37 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 451 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2BDF · Src kinase in complex with inhibitor AP23451 · 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 P12931
- Elsewhere: RCSB PDB 2BDF · PDBe 2BDF · UniProt P12931
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