MolNFT v1 · #162174 · protein
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 7F
6R13: “Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 7F”. X-ray diffraction, 5 ligands (EF2, JOK, ZN), 3 pockets (best druggability 0.63). MolNFT v1 #162174 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6R13
- Type
- protein
- Length
- 288 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- EF2, JOK, ZN, PO4, CL
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cereblon isoform 4 | protein | 108 | 8% helix, 48% strand | A4TVL0 |
| B | Cereblon isoform 4 | protein | 105 | 9% helix, 50% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 75 | 0% helix, 51% strand | A4TVL0 |
Ligands and binding sites
- EF2 · S-Thalidomide · ligand · chains A
- JOK · ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-3-phenyl-propanamide · ligand · chains B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
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 | 394 | 0.63 | 0.77 | 53 | empty |
| 2 | 79 | 0.44 | 0.80 | 20 | empty |
| 3 | 52 | 0.38 | 0.80 | 14 | EF2 |
Interfaces
2 interfaces between chains.
- A–B · 621 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6R13 · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7f · 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 6R13 · PDBe 6R13 · UniProt A4TVL0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.