MolNFT v1 · #107000 · protein
The crystal structure of human ABL1 T315I gatekeeper mutant kinase domain in complex with axitinib
4TWP · Tyrosine-protein kinase ABL1: “The crystal structure of human ABL1 T315I gatekeeper mutant kinase domain in complex with axitinib”. X-ray diffraction, 3 ligands (AXI, NI, NA), 5 pockets (best druggability 0.72). MolNFT v1 #107000 on…
- 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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