Research workbench
Structure-based Design, Synthesis, and Biological Evaluation of Imidazo[4,5-b]pyridine-2-one based p38 MAP Kinase Inhibitors by scaffold hopping - compound 10
Analyse Structure-based Design, Synthesis, and Biological Evaluation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M9L
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.45
- Source
- Homo sapiens
- Molecule
- Mitogen-activated protein kinase 14
- EC
- 2.7.11.24
- UniProt
- Q16539
- Ligands
- J9G
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.45 · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 14 (EC 2.7.11.24) | protein | 331 | 37% helix, 16% strand | Q16539 |
Ligands and binding sites
- J9G · 3-benzyl-6-[(2,4-difluorophenyl)amino]-1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one · ligand · 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 | 335 | 0.64 | 0.80 | 40 | J9G |
| 2 | 105 | 0.39 | 0.75 | 17 | empty |
| 3 | 57 | 0.34 | 0.78 | 19 | empty |
| 4 | 70 | 0.33 | 0.75 | 14 | empty |
| 5 | 71 | 0.32 | 0.75 | 18 | empty |
Compared structures
- 6M9L · Structure-based design, synthesis, and biological evaluation of… · 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 Q16539
- Elsewhere: RCSB PDB 6M9L · PDBe 6M9L · UniProt Q16539
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