MolNFT v1 · #162183 · protein
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 12A
6R1C: “Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 12A”. X-ray diffraction, 6 ligands (EF2, ASP, JOW), 5 pockets (best druggability 0.54). MolNFT v1 #162183 on GenesisL1: 3D structure, binding sites…
- PDB
- 6R1C
- Type
- protein
- Length
- 327 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- EF2, ASP, JOW, ZN, PO4, CL
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cereblon isoform 4 | protein | 110 | 8% helix, 47% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 107 | 6% helix, 50% strand | A4TVL0 |
Ligands and binding sites
- EF2 · S-Thalidomide · ligand · 2 copies · chains A, C
- ASP · Aspartic acid · ligand · chains A
- JOW · 4-[[4-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyloxymethyl]phenyl]methylamino]-4-oxidanylidene-butanoic acid · ligand · chains B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.54 | 0.88 | 17 | empty |
| 2 | 121 | 0.49 | 0.80 | 29 | PO4 |
| 3 | 53 | 0.39 | 0.80 | 12 | EF2 |
| 4 | 106 | 0.37 | 0.75 | 18 | empty |
| 5 | 106 | 0.36 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 648 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 560 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6R1C · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 12a · the same entry in another collection · chain B against B, 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 6R1C · PDBe 6R1C · UniProt A4TVL0
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