MolNFT v1 · #114744 · protein
ERK5 in complex with small molecule
5BYY · Mitogen-activated protein kinase 7: “ERK5 in complex with small molecule”. X-ray diffraction, 1 ligand (4WG), 4 pockets (best druggability 0.70). MolNFT v1 #114744 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BYY
- Type
- protein
- Length
- 338 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
- 4WG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 7 (EC 2.7.11.24) | protein | 338 | 43% helix, 13% strand | Q13164 |
Ligands and binding sites
- 4WG · 2-{[2-ethoxy-4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-B][1, 4]benzodiazepin-6-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.70 | 0.83 | 36 | 4WG |
| 2 | 101 | 0.38 | 0.75 | 14 | empty |
| 3 | 54 | 0.33 | 0.77 | 15 | empty |
| 4 | 80 | 0.31 | 0.73 | 16 | 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 5BYY · PDBe 5BYY · UniProt Q13164
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