Research workbench
CEREBLON~DDB1 bound to pomalidomide
Analyse CEREBLON~DDB1 bound to pomalidomide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D81
- Type
- protein
- Length
- 1,198 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; Protein cereblon
- UniProt
- Q16531, Q96SW2
- Ligands
- Y70, ZN
- Pockets
- 15 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 817 | 8% helix, 43% strand | Q16531 |
| B | Protein cereblon | protein | 381 | 23% helix, 22% strand | Q96SW2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.81 | 0.84 | 54 | empty |
| 2 | 831 | 0.81 | 0.83 | 68 | empty |
| 3 | 821 | 0.80 | 0.83 | 77 | empty |
| 4 | 444 | 0.71 | 0.81 | 42 | empty |
| 5 | 220 | 0.66 | 0.84 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 2533 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 8D81 · Cereblon~DDB1 bound to Pomalidomide · the same entry in another collection · chain A against A, TM-score 1.00
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q96SW2 · AlphaFold monomer V2.0 prediction for protein cereblon (Q96SW2) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q16531
- Every structure of UniProt Q96SW2
- Elsewhere: RCSB PDB 8D81 · PDBe 8D81 · UniProt Q16531 · UniProt Q96SW2
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