Research workbench
Crystal structure of P38 kinase in complex with a biphenyl amide inhibitor
Analyse Crystal structure of P38 kinase in complex with a biphenyl amide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D83
- Type
- protein
- Length
- 349 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
- GK6
- Pockets
- 6 · best druggability 0.76
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 | 349 | 40% helix, 15% strand | Q16539 |
Ligands and binding sites
- GK6 · N-{4'-[(cyclopropylmethyl)carbamoyl]-6-methylbiphenyl-3-yl}-2-morpholin-4-ylpyridine-4-carboxamide · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.76 | 0.82 | 59 | GK6 |
| 2 | 148 | 0.45 | 0.76 | 27 | empty |
| 3 | 72 | 0.36 | 0.77 | 16 | empty |
| 4 | 56 | 0.29 | 0.74 | 13 | empty |
| 5 | 61 | 0.28 | 0.73 | 16 | empty |
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 3D83 · Crystal structure of P38 kinase in complex with a biphenyl amide inhibitor · 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 3D83 · PDBe 3D83 · UniProt Q16539
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