Research workbench
Crystal structure of ERK2 in complex with an inhibitor 14K
Analyse Crystal structure of ERK2 in complex with an inhibitor 14K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XJ0
- Type
- protein
- Length
- 685 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
- P28482
- Ligands
- 41B
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 346 | 39% helix, 16% strand | P28482 |
| B | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 339 | 37% helix, 15% strand | P28482 |
Ligands and binding sites
- 41B · 1-[(1S)-1-(4-chloro-3-fluorophenyl)-2-hydroxyethyl]-4-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]pyridin-2(1H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.80 | 0.81 | 92 | 41B |
| 2 | 471 | 0.67 | 0.79 | 40 | 41B |
| 3 | 312 | 0.55 | 0.75 | 38 | empty |
| 4 | 131 | 0.48 | 0.79 | 25 | empty |
| 5 | 128 | 0.46 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 934 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4XJ0 · Crystal structure of ERK2 in complex with an inhibitor 14K · 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 P28482
- Elsewhere: RCSB PDB 4XJ0 · PDBe 4XJ0 · UniProt P28482
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