MolNFT v1 · #100187 · protein
The crystal structure of DYRK1A with a bound PYRIDO[2,3-D]PYRIMIDINE inhibitor
4MQ1 · Dual specificity tyrosine-phosphorylation-regulated kinase…: “The crystal structure of DYRK1A with a bound PYRIDO[2,3-D]PYRIMIDINE inhibitor”. X-ray diffraction, 2 ligands (2C3, SO4), 17 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 4MQ1
- Type
- protein
- Length
- 1,353 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
- 2C3, SO4
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 37% 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 | 346 | 36% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 341 | 37% helix, 18% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 329 | 37% helix, 19% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 337 | 37% helix, 18% strand | Q13627 |
Ligands and binding sites
- 2C3 · N-(5-{[(1R)-3-amino-1-(3-chlorophenyl)propyl]carbamoyl}-2-chlorophenyl)-2-methoxy-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidine-6-carboxamide · ligand · 4 copies · chains A, B, D, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.82 | 0.83 | 84 | SO4 |
| 2 | 750 | 0.75 | 0.80 | 79 | 2C3 |
| 3 | 388 | 0.65 | 0.79 | 47 | 2C3, SO4 |
| 4 | 310 | 0.65 | 0.81 | 33 | 2C3, SO4 |
| 5 | 304 | 0.65 | 0.81 | 31 | 2C3, SO4 |
Interfaces
3 interfaces between chains.
- B–D · 651 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 571 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 257 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 4MQ1 · The crystal structure of DYRK1a with a bound pyrido[2,3-d]pyrimidine inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 4MQ1 · PDBe 4MQ1 · UniProt Q13627
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