Research workbench
The crystal structure of human ABL1 T315I gatekeeper mutant kinase domain in complex with axitinib
Analyse The crystal structure of human ABL1 T315I gatekeeper mutant kinase domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TWP
- Type
- protein
- Length
- 537 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
- P00519
- Ligands
- AXI, NI, NA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 266 | 44% helix, 17% strand | P00519 |
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 271 | 46% helix, 15% strand | P00519 |
Ligands and binding sites
- AXI · Axitinib · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.72 | 0.76 | 83 | NA |
| 2 | 299 | 0.65 | 0.81 | 43 | AXI |
| 3 | 272 | 0.64 | 0.81 | 38 | AXI |
| 4 | 65 | 0.49 | 0.84 | 16 | empty |
| 5 | 61 | 0.47 | 0.84 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 314 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4TWP · The crystal structure of human abl1 T315I gatekeeper mutant kinase domain in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P00519 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00519) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P00519
- Elsewhere: RCSB PDB 4TWP · PDBe 4TWP · UniProt P00519
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