Research workbench
Crystal structure of a pyrazolopyrimidine inhibitor complex bound to mapkap kinase-2 (MK2)
Analyse Crystal structure of a pyrazolopyrimidine inhibitor complex bound to mapkap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A2C
- Type
- protein
- Length
- 3,311 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAP kinase-activated protein kinase 2
- EC
- 2.7.11.1
- UniProt
- P49137
- Ligands
- PDY, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 10 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 274 | 42% helix, 18% strand | P49137 |
| B | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 277 | 41% helix, 19% strand | P49137 |
| C | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 273 | 38% helix, 19% strand | P49137 |
| D | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 277 | 39% helix, 19% strand | P49137 |
| E, L | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 276 | 40% helix, 18% strand | P49137 |
| F | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 287 | 39% helix, 18% strand | P49137 |
| G | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 273 | 40% helix, 18% strand | P49137 |
| H | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 275 | 38% helix, 18% strand | P49137 |
| I, J | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 275 | 40% helix, 19% strand | P49137 |
| K | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 273 | 40% helix, 18% strand | P49137 |
Ligands and binding sites
- PDY · N~7~-(4-ethoxyphenyl)-6-methyl-N~5~-[(3S)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.79 | 0.94 | 30 | empty |
| 2 | 560 | 0.78 | 0.84 | 57 | empty |
| 3 | 246 | 0.69 | 0.85 | 25 | empty |
| 4 | 747 | 0.68 | 0.76 | 66 | empty |
| 5 | 676 | 0.68 | 0.76 | 68 | empty |
Interfaces
30 interfaces between chains.
- D–F · 890 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 872 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 869 Ų buried · 11 hydrogen bonds · protein-protein
- G–I · 860 Ų buried · 10 hydrogen bonds · protein-protein
- H–I · 852 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3A2C · Crystal structure of a pyrazolopyrimidine inhibitor complex bound to MAPKAP Kinase-2 (MK2) · the same entry in another collection · chain A against A, TM-score 1.00
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 P49137
- Elsewhere: RCSB PDB 3A2C · PDBe 3A2C · UniProt P49137
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