Research workbench
Discovery of potent and selective covalent inhibitors of jnk
Analyse Discovery of potent and selective covalent inhibitors of jnk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V6S
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 10
- EC
- 2.7.11.24
- UniProt
- P53779
- Ligands
- 0F0
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 10 (EC 2.7.11.24) | protein | 349 | 39% helix, 15% strand | P53779 |
| B | Mitogen-activated protein kinase 10 (EC 2.7.11.24) | protein | 341 | 40% helix, 16% strand | P53779 |
Ligands and binding sites
- 0F0 · 3-{[4-(dimethylamino)butanoyl]amino}-N-(4-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.80 | 0.84 | 90 | 0F0 |
| 2 | 741 | 0.79 | 0.83 | 78 | 0F0 |
| 3 | 94 | 0.49 | 0.82 | 22 | empty |
| 4 | 70 | 0.34 | 0.75 | 16 | empty |
| 5 | 55 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 954 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3V6S · Discovery of potent and selective covalent inhibitors of JNK · the same entry in another collection · chain A against A, TM-score 1.00
- P53779 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 10 (P53779) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P53779
- Elsewhere: RCSB PDB 3V6S · PDBe 3V6S · UniProt P53779
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