MolNFT v1 · #162181 · protein
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 20B
6R1A: “Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 20B”. X-ray diffraction, 4 ligands (EF2, JP8, ZN), 4 pockets (best druggability 0.60). MolNFT v1 #162181 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6R1A
- Type
- protein
- Length
- 331 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- EF2, JP8, ZN, PO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cereblon isoform 4 | protein | 112 | 8% helix, 46% strand | A4TVL0 |
| B | Cereblon isoform 4 | protein | 111 | 8% helix, 50% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 108 | 6% helix, 53% strand | A4TVL0 |
Ligands and binding sites
- EF2 · S-Thalidomide · ligand · 2 copies · chains A, B
- JP8 · [(2~{R})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate · ligand · chains C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.60 | 0.79 | 46 | empty |
| 2 | 65 | 0.55 | 0.88 | 18 | empty |
| 3 | 112 | 0.41 | 0.76 | 15 | empty |
| 4 | 55 | 0.39 | 0.80 | 14 | EF2 |
Interfaces
3 interfaces between chains.
- A–C · 649 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 627 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6R1A · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20b · 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 6R1A · PDBe 6R1A · UniProt A4TVL0
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