Research workbench
Structure of DCN1 bound to nacm-cov
Analyse Structure of DCN1 bound to nacm-cov in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V88
- Type
- protein
- Length
- 363 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LYSOZYME,DCN1-like protein 1
- EC
- 3.2.1.17
- UniProt
- D9IEF7, Q96GG9
- Ligands
- 8ZD
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYSOZYME,DCN1-like protein 1 (EC 3.2.1.17) | protein | 363 | 63% helix, 7% strand | D9IEF7, Q96GG9 |
Ligands and binding sites
- 8ZD · N-{2-[({1-[(2R)-pentan-2-yl]piperidin-4-yl}{[3-(trifluoromethyl)phenyl]carbamoyl}amino) methyl]phenyl}propanamide · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.60 | 0.83 | 24 | 8ZD |
| 2 | 352 | 0.59 | 0.76 | 38 | empty |
| 3 | 176 | 0.43 | 0.74 | 26 | empty |
| 4 | 101 | 0.39 | 0.76 | 25 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 D9IEF7
- Every structure of UniProt Q96GG9
- Elsewhere: RCSB PDB 5V88 · PDBe 5V88 · UniProt D9IEF7 · UniProt Q96GG9
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