Research workbench
ERK5 in complex with small molecule
Analyse ERK5 in complex with small molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BYZ
- Type
- protein
- Length
- 348 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 7
- EC
- 2.7.11.24
- UniProt
- Q13164
- Ligands
- 4WE
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 7 (EC 2.7.11.24) | protein | 348 | 45% helix, 13% strand | Q13164 |
Ligands and binding sites
- 4WE · 4-({5-fluoro-4-[2-methyl-1-(propan-2-yl)-1H-imidazol-5-yl]pyrimidin-2-yl}amino)-N-[2-(piperidin-1-yl) ethyl]benzamide · ligand · chains A
- GOL · Glycerol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.68 | 0.82 | 45 | 4WE |
| 2 | 53 | 0.44 | 0.84 | 17 | empty |
| 3 | 100 | 0.40 | 0.77 | 23 | empty |
| 4 | 66 | 0.31 | 0.74 | 15 | empty |
| 5 | 56 | 0.27 | 0.73 | 12 | empty |
Compared structures
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 Q13164
- Elsewhere: RCSB PDB 5BYZ · PDBe 5BYZ · UniProt Q13164
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