MolNFT v1 · #100188 · protein
The crystal structure of DYRK1A with a bound PYRIDO[2,3-D]PYRIMIDINE inhibitor
4MQ2 · 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 (2C4, SO4), 17 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 4MQ2
- 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
- 2C4, SO4
- Pockets
- 17 · best druggability 0.81
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 | 344 | 36% helix, 17% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 339 | 35% helix, 18% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 340 | 38% helix, 18% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 330 | 37% helix, 18% strand | Q13627 |
Ligands and binding sites
- 2C4 · methyl 4-chloro-3-{[(2-methoxy-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl)carbonyl]amino}benzoate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, 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 | 990 | 0.81 | 0.82 | 63 | SO4 |
| 2 | 843 | 0.73 | 0.78 | 83 | 2C4 |
| 3 | 346 | 0.66 | 0.80 | 41 | 2C4 |
| 4 | 334 | 0.65 | 0.80 | 42 | 2C4 |
| 5 | 222 | 0.64 | 0.83 | 25 | 2C4 |
Interfaces
3 interfaces between chains.
- B–D · 587 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 512 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 253 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 4MQ2 · 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 0.99
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 4MQ2 · PDBe 4MQ2 · UniProt Q13627
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