Research workbench
Structure of CDL2.3B, a computationally designed vitamin-D3 binder
Analyse Structure of CDL2.3B, a computationally designed vitamin-D3 binder in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IEP
- Type
- protein
- Length
- 121 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CDL2.3B
- Ligands
- VDY
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CDL2.3B | protein | 121 | 29% helix, 49% strand | — |
Ligands and binding sites
- VDY · 3-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexanol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.73 | 0.88 | 25 | VDY |
Compared structures
- 5IEP · Structure of CDL2.3b, a computationally designed Vitamin-D3 binder · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5IEP · PDBe 5IEP
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