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
- 3V6R
- Type
- protein
- Length
- 697 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
- CQQ
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 10 (EC 2.7.11.24) | protein | 350 | 39% helix, 15% strand | P53779 |
| B | Mitogen-activated protein kinase 10 (EC 2.7.11.24) | protein | 347 | 39% helix, 17% strand | P53779 |
Ligands and binding sites
- CQQ · 4-{[4-(dimethylamino)butanoyl]amino}-N-(3-{[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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.85 | 0.86 | 103 | CQQ |
| 2 | 562 | 0.71 | 0.80 | 64 | CQQ |
| 3 | 67 | 0.54 | 0.87 | 16 | empty |
| 4 | 64 | 0.44 | 0.82 | 19 | empty |
| 5 | 72 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 895 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3V6R · 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 0.97
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 3V6R · PDBe 3V6R · UniProt P53779
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