MolNFT v1 · #147614 · protein
DYRK1A in complex with XMD8-49
6EIL: “DYRK1A in complex with XMD8-49”. X-ray diffraction, 1 ligand (B6B), 9 pockets (best druggability 0.87). MolNFT v1 #147614 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EIL
- Type
- protein
- Length
- 1,348 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DYRK1A
- UniProt
- Q13627
- Ligands
- B6B
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DYRK1A | protein | 342 | 36% helix, 18% strand | Q13627 |
| B | DYRK1A | protein | 340 | 34% helix, 18% strand | Q13627 |
| C | DYRK1A | protein | 333 | 38% helix, 16% strand | Q13627 |
| D | DYRK1A | protein | 333 | 38% helix, 19% strand | Q13627 |
Ligands and binding sites
- B6B · [3-azanyl-6-(5-azanyl-2-methoxy-phenyl)pyrazin-2-yl]-pyridin-3-yl-methanone · ligand · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.87 | 0.88 | 131 | empty |
| 2 | 1163 | 0.84 | 0.84 | 116 | empty |
| 3 | 834 | 0.77 | 0.80 | 79 | B6B |
| 4 | 908 | 0.76 | 0.79 | 92 | empty |
| 5 | 561 | 0.73 | 0.81 | 58 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1221 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1191 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 964 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 854 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
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 Q13627
- Elsewhere: RCSB PDB 6EIL · PDBe 6EIL · UniProt Q13627
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