MolNFT v1 · #147608 · protein
DYRK1A in complex with XMD7-117
6EIF · Dual specificity tyrosine-phosphorylation-regulated kinase…: “DYRK1A in complex with XMD7-117”. X-ray diffraction, 1 ligand (B5T), 11 pockets (best druggability 0.83). MolNFT v1 #147608 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6EIF
- Type
- protein
- Length
- 1,330 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity tyrosine-phosphorylation-regulated kinase 1A
- EC
- 2.7.12.1
- UniProt
- Q13627
- Ligands
- B5T
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 344 | 34% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 338 | 33% helix, 17% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 317 | 36% helix, 18% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 331 | 35% helix, 19% strand | Q13627 |
Ligands and binding sites
- B5T · 4-(3-pyridin-3-yl-1~{H}-pyrrolo[2,3-b]pyridin-5-yl) benzenesulfonamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.83 | 0.90 | 73 | empty |
| 2 | 346 | 0.82 | 0.91 | 51 | empty |
| 3 | 1104 | 0.81 | 0.82 | 113 | empty |
| 4 | 980 | 0.77 | 0.79 | 105 | B5T |
| 5 | 713 | 0.76 | 0.81 | 78 | B5T |
Interfaces
6 interfaces between chains.
- A–B · 1238 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1196 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 957 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 658 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 28 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 6EIF · PDBe 6EIF · UniProt Q13627
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