Research workbench
DCN1 bound to 8
Analyse DCN1 bound to 8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XOM
- Type
- protein
- Length
- 357 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme, DCN1-like protein 1 chimera
- EC
- 3.2.1.17
- UniProt
- D9IEF7, Q96GG9
- Ligands
- H8V
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme, DCN1-like protein 1 chimera (EC 3.2.1.17) | protein | 357 | 62% helix, 7% strand | D9IEF7, Q96GG9 |
Ligands and binding sites
- H8V · (2R)-N-[(2S)-2-cyclohexyl-2-({N-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alanyl}amino)ethyl]-2-methyl-4-(morpholin-4-yl)butanamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.67 | 0.86 | 25 | H8V |
| 2 | 346 | 0.57 | 0.76 | 46 | empty |
| 3 | 74 | 0.30 | 0.74 | 15 | empty |
| 4 | 60 | 0.27 | 0.73 | 13 | EDO |
| 5 | 58 | 0.26 | 0.72 | 14 | 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 6XOM · PDBe 6XOM · UniProt D9IEF7 · UniProt Q96GG9
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