MolNFT v1 · #112546 · protein
Vx-680/MK-0457 binds to human ABL1 also in inactive dfg conformations.
4ZOG · Tyrosine-protein kinase ABL1: “Vx-680/MK-0457 binds to human ABL1 also in inactive dfg conformations.”. X-ray diffraction, 1 ligand (VX6), 5 pockets (best druggability 0.78). MolNFT v1 #112546 on GenesisL1: 3D structure, binding…
- PDB
- 4ZOG
- 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
- VX6
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 269 | 43% helix, 18% strand | P00519 |
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 268 | 43% helix, 18% strand | P00519 |
Ligands and binding sites
- VX6 · Cyclopropanecarboxylic acid {4-[4-(4-methyl-piperazin-1-yl)-6-(5-methyl-2H-pyrazol-3-ylamino)-pyrimidin-2-ylsulfanyl]-phenyl}-amide · ligand · 2 copies · chains A, B
- MXE · 2-methoxyethanol · additive · 3 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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 | 758 | 0.78 | 0.81 | 70 | VX6, MXE, MES |
| 2 | 411 | 0.70 | 0.81 | 46 | VX6 |
| 3 | 88 | 0.52 | 0.83 | 22 | empty |
| 4 | 67 | 0.49 | 0.84 | 15 | empty |
| 5 | 160 | 0.43 | 0.74 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 856 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4ZOG · VX-680/MK-0457 binds to human ABL1 also in inactive DFG conformations. · 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 4ZOG · PDBe 4ZOG · UniProt P00519
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