MolNFT v1 · #170854 · protein
Biochemical, cellular and structural characterization of novel ERK3 inhibitors
6YKY · Mitogen-activated protein kinase 6: “Biochemical, cellular and structural characterization of novel ERK3 inhibitors”. X-ray diffraction, 1 ligand (OWQ), 18 pockets (best druggability 0.85). MolNFT v1 #170854 on GenesisL1: 3D…
- PDB
- 6YKY
- Type
- protein
- Length
- 1,154 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
- OWQ
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 6 (EC 2.7.11.24) | protein | 281 | 40% helix, 18% strand | Q16659 |
| B | Mitogen-activated protein kinase 6 (EC 2.7.11.24) | protein | 289 | 37% helix, 18% strand | Q16659 |
| C | Mitogen-activated protein kinase 6 (EC 2.7.11.24) | protein | 283 | 37% helix, 18% strand | Q16659 |
| D | Mitogen-activated protein kinase 6 (EC 2.7.11.24) | protein | 301 | 37% helix, 17% strand | Q16659 |
Ligands and binding sites
- OWQ · 3-(4-methoxyphenyl)-~{N}-[(3~{R})-1-pyridin-4-ylpyrrolidin-3-yl]-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.85 | 0.86 | 112 | OWQ |
| 2 | 1075 | 0.76 | 0.79 | 90 | OWQ |
| 3 | 251 | 0.71 | 0.86 | 29 | empty |
| 4 | 474 | 0.70 | 0.81 | 48 | empty |
| 5 | 400 | 0.65 | 0.79 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1284 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 968 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 842 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 358 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6YKY · 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 C 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 6YKY · PDBe 6YKY · UniProt Q16659
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