Research workbench
Biochemical, cellular and structural characterization of novel ERK3 inhibitors
Analyse Biochemical, cellular and structural characterization of novel ERK3 inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YLC
- Type
- protein
- Length
- 1,157 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 6
- EC
- 2.7.11.24
- UniProt
- Q16659
- Ligands
- OXW
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 6 (EC 2.7.11.24) | protein | 282 | 38% helix, 18% strand | Q16659 |
| B | Mitogen-activated protein kinase 6 (EC 2.7.11.24) | protein | 292 | 38% helix, 17% strand | Q16659 |
| C | Mitogen-activated protein kinase 6 (EC 2.7.11.24) | protein | 280 | 40% helix, 16% strand | Q16659 |
| D | Mitogen-activated protein kinase 6 (EC 2.7.11.24) | protein | 303 | 39% helix, 18% strand | Q16659 |
Ligands and binding sites
- OXW · 5-fluoranyl-2-[5-[[1-(1-methylpiperidin-4-yl)pyrazol-4-yl]amino]-[1,2,3]triazolo[4,5-d]pyrimidin-3-yl]benzenecarbonitrile · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.84 | 0.85 | 119 | OXW |
| 2 | 1052 | 0.82 | 0.83 | 101 | OXW |
| 3 | 558 | 0.73 | 0.81 | 49 | empty |
| 4 | 292 | 0.66 | 0.82 | 40 | empty |
| 5 | 393 | 0.65 | 0.78 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1162 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1115 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 919 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 272 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YLC · Biochemical, Cellular and Structural Characterization of Novel ERK3 Inhibitors · the same entry in another collection · chain D against D, TM-score 1.00
- Q16659 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 6 (Q16659) · 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 Q16659
- Elsewhere: RCSB PDB 6YLC · PDBe 6YLC · UniProt Q16659
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