MolNFT v1 · #76657 · protein
The crystal structure of human ABL1 kinase domain in complex with dcc- 2036
3QRI · Tyrosine-protein kinase ABL1: “The crystal structure of human ABL1 kinase domain in complex with dcc- 2036”. X-ray diffraction, 2 ligands (919, NA), 8 pockets (best druggability 0.76). MolNFT v1 #76657 on GenesisL1: 3D structure…
- PDB
- 3QRI
- 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
- 919, NA
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 275 | 41% helix, 17% strand | P00519 |
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 262 | 42% helix, 17% strand | P00519 |
Ligands and binding sites
- 919 · 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.76 | 0.85 | 51 | 919 |
| 2 | 404 | 0.75 | 0.84 | 49 | 919 |
| 3 | 725 | 0.70 | 0.77 | 47 | empty |
| 4 | 238 | 0.57 | 0.78 | 35 | empty |
| 5 | 61 | 0.50 | 0.85 | 15 | NA |
Interfaces
1 interface between chains.
- A–B · 316 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3QRI · The crystal structure of human abl1 kinase domain in complex with DCC-2036 · 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 0.92
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 3QRI · PDBe 3QRI · UniProt P00519
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