MolNFT v1 · #88692 · protein
Structure of melk in complex with inhibitors
4D2W · Maternal embryonic leucine zipper kinase: “Structure of melk in complex with inhibitors”. X-ray diffraction, 1 ligand (NF5), 16 pockets (best druggability 0.82). MolNFT v1 #88692 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4D2W
- Type
- protein
- Length
- 1,276 residues
- Chains
- 4
- 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
- NF5
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 43% 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 | 314 | 43% helix, 16% strand | Q14680 |
| B | Maternal embryonic leucine zipper kinase (EC 2.7.11.1, 2.7.10.2) | protein | 323 | 41% helix, 15% strand | Q14680 |
| C | Maternal embryonic leucine zipper kinase (EC 2.7.11.1, 2.7.10.2) | protein | 313 | 43% helix, 16% strand | Q14680 |
| D | Maternal embryonic leucine zipper kinase (EC 2.7.11.1, 2.7.10.2) | protein | 326 | 44% helix, 15% strand | Q14680 |
Ligands and binding sites
- NF5 · 4-bromo-N-(2,3,4,5-tetrahydro-1H-3-benzazepin-7-yl)benzamide · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.82 | 0.89 | 67 | NF5 |
| 2 | 688 | 0.82 | 0.86 | 85 | NF5 |
| 3 | 657 | 0.82 | 0.86 | 72 | NF5 |
| 4 | 462 | 0.81 | 0.88 | 66 | NF5 |
| 5 | 600 | 0.77 | 0.83 | 66 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1424 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1277 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 497 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 392 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 4D2W · PDBe 4D2W · UniProt Q14680
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