MolNFT v1 · #147620 · protein
DYRK1A in complex with XMD15-27-2
6EIR · Dual specificity tyrosine-phosphorylation-regulated kinase…: “DYRK1A in complex with XMD15-27-2”. X-ray diffraction, 1 ligand (B6H), 13 pockets (best druggability 0.86). MolNFT v1 #147620 on GenesisL1: 3D structure, binding sites…
- PDB
- 6EIR
- Type
- protein
- Length
- 1,343 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
- B6H
- Pockets
- 13 · best druggability 0.86
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 | 37% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 335 | 37% helix, 18% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 333 | 37% helix, 17% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 333 | 34% helix, 19% strand | Q13627 |
Ligands and binding sites
- B6H · ~{N}-[4-[[4-azanyl-2-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]-1,3-thiazol-5-yl]carbonyl]phenyl]propanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.86 | 0.87 | 111 | empty |
| 2 | 916 | 0.85 | 0.86 | 108 | empty |
| 3 | 1052 | 0.80 | 0.81 | 107 | B6H |
| 4 | 728 | 0.76 | 0.81 | 63 | B6H |
| 5 | 801 | 0.75 | 0.79 | 79 | B6H |
Interfaces
6 interfaces between chains.
- C–D · 1305 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1298 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 982 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 965 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 43 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 6EIR · PDBe 6EIR · UniProt Q13627
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