MolNFT v1 · #147742 · protein
Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor
6EMH · Mitogen-activated protein kinase 10: “Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor”. X-ray diffraction, 3 ligands (BGE, C15, CL), 10 pockets (best druggability 0.77). MolNFT v1 #147742 on GenesisL1: 3D…
- PDB
- 6EMH
- Type
- protein
- Length
- 1,353 residues
- Chains
- 4
- 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
- BGE, C15, CL
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mitogen-activated protein kinase 10 (EC 2.7.11.24) | protein | 344 | 42% helix, 15% strand | P53779 |
| C | Mitogen-activated protein kinase 10 (EC 2.7.11.24) | protein | 334 | 41% helix, 16% strand | P53779 |
| D | Mitogen-activated protein kinase 10 (EC 2.7.11.24) | protein | 331 | 43% helix, 16% strand | P53779 |
Ligands and binding sites
- BGE · 4-(4-methyl-1~{H}-imidazol-5-yl)-~{N}-(4-morpholin-4-ylphenyl)pyridin-2-amine · ligand · 4 copies · chains A, B, C, D
- C15 · N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate · ligand · 2 copies · chains A, C, B
- CL · Chloride ion · ion · 3 copies · chains A, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.77 | 0.79 | 111 | C15, PEG, BGE |
| 2 | 595 | 0.75 | 0.82 | 60 | BGE |
| 3 | 334 | 0.67 | 0.81 | 24 | empty |
| 4 | 510 | 0.65 | 0.77 | 53 | BGE |
| 5 | 312 | 0.59 | 0.77 | 39 | BGE |
Interfaces
2 interfaces between chains.
- A–C · 939 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 441 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 6EMH · Crystal structure of JNK3 in complex with a pyridinylimidazole 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 P53779
- Elsewhere: RCSB PDB 6EMH · PDBe 6EMH · UniProt P53779
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