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 1
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
- 6M95
- Type
- protein
- Length
- 333 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Homo sapiens
- Molecule
- Mitogen-activated protein kinase 14
- EC
- 2.7.11.24
- UniProt
- Q16539
- Ligands
- J8S
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 14 (EC 2.7.11.24) | protein | 333 | 40% helix, 15% strand | Q16539 |
Ligands and binding sites
- J8S · (4-benzylpiperidin-1-yl)[2-methoxy-4-(methylsulfanyl) phenyl]methanone · 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 | 375 | 0.69 | 0.81 | 47 | J8S |
| 2 | 92 | 0.41 | 0.78 | 18 | empty |
| 3 | 100 | 0.36 | 0.73 | 16 | empty |
| 4 | 59 | 0.31 | 0.76 | 19 | empty |
| 5 | 56 | 0.28 | 0.74 | 14 | empty |
Compared structures
- 6M95 · 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 6M95 · PDBe 6M95 · UniProt Q16539
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