MolNFT v1 · #115085 · protein
NEDD4 hect with covalently bound indole-based inhibitor
5C91 · E3 ubiquitin-protein ligase NEDD4: “NEDD4 hect with covalently bound indole-based inhibitor”. X-ray diffraction, 1 ligand (4YU), 4 pockets (best druggability 0.71). MolNFT v1 #115085 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5C91
- Type
- protein
- Length
- 375 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase NEDD4
- EC
- 6.3.2.-
- UniProt
- P46934
- Ligands
- 4YU
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-) | protein | 375 | 51% helix, 13% strand | P46934 |
Ligands and binding sites
- 4YU · methyl (2E)-4-{[(5-methoxy-1,2-dimethyl-1H-indol-3-yl)carbonyl]amino}but-2-enoate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.71 | 0.77 | 70 | empty |
| 2 | 139 | 0.48 | 0.78 | 31 | empty |
| 3 | 58 | 0.28 | 0.74 | 13 | empty |
| 4 | 52 | 0.26 | 0.73 | 12 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5C91 · NEDD4 HECT with covalently bound indole-based inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P46934 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase NEDD4 (P46934) · a predicted model of the same protein · chain A against A, TM-score 0.71
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 P46934
- Elsewhere: RCSB PDB 5C91 · PDBe 5C91 · UniProt P46934
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