Research workbench
Structural analysis of dfg-in and dfg-out dual src-abl inhibitors sharing a common vinyl purine template
Analyse Structural analysis of dfg-in and dfg-out dual src-abl inhibitors sharing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KF4
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase ABL1
- EC
- 2.7.10.2
- UniProt
- P00520
- Ligands
- B90
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 281 | 44% helix, 17% strand | P00520 |
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 270 | 44% helix, 17% strand | P00520 |
Ligands and binding sites
- B90 · N-[4-(dimethylphosphoryl)phenyl]-9-[(E)-2-(5-methyl-1H-indazol-4-yl)ethenyl]-9H-purin-6-amine · ligand · 2 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 | 1162 | 0.75 | 0.78 | 91 | B90 |
| 2 | 289 | 0.66 | 0.82 | 38 | B90 |
| 3 | 295 | 0.60 | 0.78 | 43 | empty |
| 4 | 54 | 0.47 | 0.84 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 477 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3KF4 · Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P00520 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00520) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P00520
- Elsewhere: RCSB PDB 3KF4 · PDBe 3KF4 · UniProt P00520
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