MolNFT v1 · #121495 · protein
Cereblon in complex with DDB1, cc-885, and GSPT1
5HXB · Eukaryotic peptide chain release factor GTP-binding subunit…: “Cereblon in complex with DDB1, cc-885, and GSPT1”. X-ray diffraction, 2 ligands (85C, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #121495 on GenesisL1: 3D…
- PDB
- 5HXB
- Type
- protein
- Length
- 3,296 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic peptide chain release factor GTP-binding subunit ERF3A; DNA damage-binding…
- UniProt
- P15170, Q16531, Q96SW2
- Ligands
- 85C, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Eukaryotic peptide chain release factor GTP-binding subunit ERF3A | protein | 195 | 0% helix, 46% strand | P15170 |
| Y | DNA damage-binding protein 1 | protein | 1080 | 5% helix, 53% strand | Q16531 |
| Z | Protein cereblon | protein | 380 | 27% helix, 30% strand | Q96SW2 |
| B | DNA damage-binding protein 1 | protein | 1075 | 5% helix, 53% strand | Q16531 |
| C | Protein cereblon | protein | 370 | 27% helix, 31% strand | Q96SW2 |
| A | Eukaryotic peptide chain release factor GTP-binding subunit ERF3A | protein | 196 | 0% helix, 48% strand | P15170 |
Ligands and binding sites
- 85C · 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea · ligand · 2 copies · chains X, Z, C, A
- ZN · Zinc ion · metal · 2 copies · chains Z, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.86 | 0.87 | 83 | empty |
| 2 | 1199 | 0.85 | 0.86 | 106 | empty |
| 3 | 1078 | 0.80 | 0.81 | 115 | empty |
| 4 | 848 | 0.78 | 0.81 | 88 | 85C |
| 5 | 801 | 0.77 | 0.81 | 90 | 85C |
Interfaces
5 interfaces between chains.
- Y–Z · 2236 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2180 Ų buried · 11 hydrogen bonds · protein-protein
- X–Z · 698 Ų buried · 6 hydrogen bonds · protein-protein
- C–A · 654 Ų buried · 5 hydrogen bonds · protein-protein
- Y–B · 508 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5HXB · Cereblon in complex with DDB1, CC-885, and GSPT1 · 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 C against A, TM-score 0.99
- P15170 · AlphaFold monomer V2.0 prediction for eukaryotic peptide chain release factor GTP-binding… · a predicted model of the same protein · chain X against A, TM-score 0.96
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain Y against A, TM-score 0.85
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 P15170
- Every structure of UniProt Q16531
- Every structure of UniProt Q96SW2
- Elsewhere: RCSB PDB 5HXB · PDBe 5HXB · UniProt P15170 · UniProt Q16531 · UniProt Q96SW2
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