MolNFT v2 · #138851 · protein
MAP4K4 in complex with inhibitor compound 12 (N3-methyl-10-(3-methyl-3-(5-methyloxazol-2-yl)but-1-yn-1-yl)-6,7-dihydro-5H-5,7-methanobenzo[c]imidazo[1,2-a]azepine-2,3-dicarboxamide)
5W5Q · Mitogen-activated protein kinase kinase kinase kinase 4: “MAP4K4 in complex with inhibitor compound 12 (N3-methyl-10-(3-methyl-3-(5-methyloxazol-2-yl)but-1-yn-1-yl)-6,7…”. X-ray diffraction at 2.33, 1 ligand (9X4), 6 pockets (best…
- PDB
- 5W5Q
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.33
- Source
- Homo sapiens
- Molecule
- Mitogen-activated protein kinase kinase kinase kinase 4
- EC
- 2.7.11.1
- UniProt
- O95819
- Ligands
- 9X4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.33 · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase kinase 4 (EC 2.7.11.1) | protein | 291 | 38% helix, 18% strand | O95819 |
| B | Mitogen-activated protein kinase kinase kinase kinase 4 (EC 2.7.11.1) | protein | 297 | 38% helix, 18% strand | O95819 |
Ligands and binding sites
- 9X4 · (5s,7s)-N~3~-methyl-10-[3-methyl-3-(5-methyl-1,3-oxazol-2-yl)but-1-yn-1-yl]-6,7-dihydro-5H-5,7-methanoimidazo[2,1-a][2]benzazepine-2,3-dicarboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.84 | 0.85 | 118 | 9X4 |
| 2 | 1075 | 0.84 | 0.84 | 89 | empty |
| 3 | 122 | 0.62 | 0.86 | 25 | empty |
| 4 | 60 | 0.38 | 0.80 | 16 | empty |
| 5 | 61 | 0.36 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1637 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5W5Q · MAP4K4 in complex with inhibitor compound 12 (N3-methyl-10-(3-methyl… · the same entry in another collection · chain A against A, TM-score 1.00
- O95819 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O95819
- Elsewhere: RCSB PDB 5W5Q · PDBe 5W5Q · UniProt O95819
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