MolNFT v1 · #191340 · protein
CEREBLON~DDB1 bound to iberdomide and ikaros ZF1-2-3
8D80 · DNA damage-binding protein 1: “CEREBLON~DDB1 bound to iberdomide and ikaros ZF1-2-3”. Electron microscopy, 2 ligands (8W7, ZN), 20 pockets (best druggability 0.82). MolNFT v1 #191340 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8D80
- Type
- protein
- Length
- 1,542 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; Protein cereblon; DNA-binding protein ikaros
- UniProt
- Q16531, Q96SW2, Q13422
- Ligands
- 8W7, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1132 | 5% helix, 48% strand | Q16531 |
| B | Protein cereblon | protein | 381 | 24% helix, 25% strand | Q96SW2 |
| C | DNA-binding protein ikaros | protein | 29 | 34% helix, 7% strand | Q13422 |
Ligands and binding sites
- 8W7 · (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione · ligand · chains B, C
- ZN · Zinc ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.82 | 0.83 | 117 | empty |
| 2 | 886 | 0.82 | 0.83 | 50 | empty |
| 3 | 1012 | 0.81 | 0.82 | 98 | empty |
| 4 | 785 | 0.75 | 0.80 | 91 | empty |
| 5 | 811 | 0.75 | 0.79 | 82 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2416 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 377 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 8D80 · Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q96SW2 · AlphaFold monomer V2.0 prediction for protein cereblon (Q96SW2) · a predicted model of the same protein · chain B against A, TM-score 0.97
- 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 0.87
- Q13422 · AlphaFold monomer V2.0 prediction for DNA-binding protein ikaros (Q13422) · a predicted model of the same protein · chain C against A, TM-score 0.65
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
- Every structure of UniProt Q13422
- Elsewhere: RCSB PDB 8D80 · PDBe 8D80 · UniProt Q16531 · UniProt Q96SW2 · UniProt Q13422
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