MolNFT v1 · #185371 · protein
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with iberdomide (cc-220)
7PS9: “Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with iberdomide (cc-220)”. X-ray diffraction, 2 ligands (8W7, ZN), 3 pockets (best druggability 0.57). MolNFT v1 #185371 on GenesisL1: 3D structure, binding sites…
- PDB
- 7PS9
- Type
- protein
- Length
- 303 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- 8W7, ZN
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cereblon isoform 4 | protein | 108 | 6% helix, 50% strand | A4TVL0 |
| B | Cereblon isoform 4 | protein | 105 | 6% helix, 53% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 90 | 7% helix, 47% strand | A4TVL0 |
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 · 3 copies · chains A, C, B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.57 | 0.77 | 44 | empty |
| 2 | 56 | 0.39 | 0.80 | 15 | 8W7 |
| 3 | 52 | 0.35 | 0.78 | 14 | 8W7 |
Interfaces
2 interfaces between chains.
- A–B · 580 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7PS9 · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Iberdomide… · 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
- Every structure of UniProt A4TVL0
- Elsewhere: RCSB PDB 7PS9 · PDBe 7PS9 · UniProt A4TVL0
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