MolNFT v1 · #116577 · protein
MAP4K4 in complex with an inhibitor
5DI1 · Mitogen-activated protein kinase kinase kinase kinase 4: “MAP4K4 in complex with an inhibitor”. X-ray diffraction, 1 ligand (5DF), 6 pockets (best druggability 0.76). MolNFT v1 #116577 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DI1
- Type
- protein
- Length
- 585 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase kinase kinase 4
- EC
- 2.7.11.1
- UniProt
- O95819
- Ligands
- 5DF
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase kinase 4 (EC 2.7.11.1) | protein | 285 | 38% helix, 16% strand | O95819 |
| B | Mitogen-activated protein kinase kinase kinase kinase 4 (EC 2.7.11.1) | protein | 300 | 36% helix, 17% strand | O95819 |
Ligands and binding sites
- 5DF · 4-{6-amino-5-[4-(methylsulfonyl)phenyl]pyridin-3-yl}phenol · 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 | 468 | 0.76 | 0.84 | 60 | 5DF |
| 2 | 358 | 0.70 | 0.83 | 48 | empty |
| 3 | 151 | 0.55 | 0.81 | 27 | empty |
| 4 | 66 | 0.40 | 0.79 | 18 | empty |
| 5 | 57 | 0.34 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1418 Ų buried · 16 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 O95819
- Elsewhere: RCSB PDB 5DI1 · PDBe 5DI1 · UniProt O95819
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