Research workbench
DYRK1A in complex with XMD14-124
Analyse DYRK1A in complex with XMD14-124 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EIQ
- Type
- protein
- Length
- 1,348 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
- B6Z
- 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 | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 342 | 36% helix, 19% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 340 | 36% helix, 19% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 333 | 35% helix, 17% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 333 | 36% helix, 19% strand | Q13627 |
Ligands and binding sites
- B6Z · [4-azanyl-2-[[2-methoxy-4-(4-methylpiperazin-1-yl) phenyl]amino]-1,3-thiazol-5-yl]-phenyl-methanone · ligand · 4 copies · chains A, B, C, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.87 | 0.88 | 131 | empty |
| 2 | 937 | 0.83 | 0.85 | 87 | empty |
| 3 | 916 | 0.80 | 0.82 | 79 | B6Z |
| 4 | 1050 | 0.77 | 0.79 | 100 | B6Z |
| 5 | 639 | 0.77 | 0.82 | 71 | B6Z |
Interfaces
6 interfaces between chains.
- A–B · 1296 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1262 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 982 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 818 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 disulfide (phosphorylation, disulfide).
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 6EIQ · PDBe 6EIQ · UniProt Q13627
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