Research workbench
A double mutant rat ERK2 in complex with a PYRAZOLO[3,4-D]PYRIMIDINE inhibitor
Analyse A double mutant rat ERK2 in complex with a PYRAZOLO[3,4-D]PYRIMIDINE inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N4S
- Type
- protein
- Length
- 679 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 1
- EC
- 2.7.11.24
- UniProt
- P63086
- Ligands
- 2H1
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 342 | 39% helix, 15% strand | P63086 |
| B | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 337 | 40% helix, 15% strand | P63086 |
Ligands and binding sites
- 2H1 · 3-[2-(benzyloxy)-8-methylquinolin-6-yl]-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.78 | 0.82 | 76 | 2H1 |
| 2 | 385 | 0.74 | 0.84 | 35 | 2H1 |
| 3 | 500 | 0.67 | 0.78 | 51 | empty |
| 4 | 230 | 0.54 | 0.77 | 25 | empty |
| 5 | 163 | 0.52 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 436 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4N4S · A Double Mutant Rat Erk2 in Complex With a Pyrazolo[3,4-d]pyrimidine Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P63086 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 1 (P63086) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P63086
- Elsewhere: RCSB PDB 4N4S · PDBe 4N4S · UniProt P63086
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