Research workbench
P38 alpha MAP kinase inhibitor based on heterobicyclic scaffolds
Analyse P38 alpha MAP kinase inhibitor based on heterobicyclic scaffolds in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QD9
- Type
- protein
- Length
- 330 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 14
- EC
- 2.7.11.24
- UniProt
- Q16539
- Ligands
- LGF
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 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 | 330 | 40% helix, 15% strand | Q16539 |
Ligands and binding sites
- LGF · 1-[5-[[3-[2,4-bis(fluoranyl)phenyl]-6,8-dihydro-5~{H}-imidazo[1,5-a]pyrazin-7-yl]carbonyl]-6-methoxy-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]-2-[(3~{R})-3-oxidanylpyrrolidin-1-yl]ethane-1,2-dione · 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 | 214 | 0.64 | 0.83 | 31 | LGF |
| 2 | 77 | 0.35 | 0.76 | 18 | empty |
| 3 | 95 | 0.34 | 0.74 | 18 | empty |
| 4 | 57 | 0.29 | 0.74 | 15 | empty |
Compared structures
- 2QD9 · P38 Alpha Map Kinase inhibitor based on heterobicyclic scaffolds · 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 2QD9 · PDBe 2QD9 · UniProt Q16539
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