MolNFT v1 · #150516 · protein
Crystal structure of maternal embryonic leucine zipper kinase (melk) in complex with dorsomorphin (compound C)
6GVX: “Crystal structure of maternal embryonic leucine zipper kinase (melk) in complex with dorsomorphin (compound C)”. X-ray diffraction, 1 ligand (TAK), 6 pockets (best druggability 0.80). MolNFT v1 #150516 on GenesisL1: 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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