Research workbench
Crystal structure of maternal embryonic leucine zipper kinase (melk) in complex with dorsomorphin (compound C)
Analyse Crystal structure of maternal embryonic leucine zipper kinase (melk) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GVX
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maternal embryonic leucine zipper kinase
- EC
- 2.7.11.1, 2.7.10.2
- UniProt
- Q14680
- Ligands
- TAK
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maternal embryonic leucine zipper kinase (EC 2.7.11.1, 2.7.10.2) | protein | 315 | 40% helix, 15% strand | Q14680 |
| B | Maternal embryonic leucine zipper kinase (EC 2.7.11.1, 2.7.10.2) | protein | 319 | 41% helix, 15% strand | Q14680 |
Ligands and binding sites
- TAK · 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.80 | 0.85 | 57 | TAK |
| 2 | 585 | 0.79 | 0.85 | 68 | TAK |
| 3 | 336 | 0.65 | 0.80 | 35 | empty |
| 4 | 264 | 0.62 | 0.80 | 33 | empty |
| 5 | 58 | 0.38 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1460 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6GVX · Crystal structure of Maternal Embryonic Leucine Zipper Kinase (MELK) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q14680 · AlphaFold monomer V2.0 prediction for maternal embryonic leucine zipper kinase (Q14680) · 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 Q14680
- Elsewhere: RCSB PDB 6GVX · PDBe 6GVX · UniProt Q14680
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