› 8beb

X-ray diffraction
3.18Å resolution

Ternary complex between VCB, BRD4-BD1 and PROTAC 49

Released:
DOI: 10.2210/pdb8beb/pdb
PDB entry 8beb coloured by chain, front view.
PDB entry 8beb coloured by chain, side view.
PDB entry 8beb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Systematic Potency & Property Assessment of VHL Ligands and Implications on PROTAC Design.
Krieger J, Sorell FJ, Wegener AA, Leuthner B, Machrouhi-Porcher F, Hecht M, Leibrock EM, Mueller JE, Eisert J, Hartung IV, Schlesiger S
ChemMedChem (2023)
PMID: 36749883

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-130120 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Elongin-B Chain: A
Molecule details ›
Chain: A
Length: 104 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15370 (Residues: 1-104; Coverage: 88%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family
Elongin-C Chain: B
Molecule details ›
Chain: B
Length: 97 amino acids
Theoretical weight: 10.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15369 (Residues: 17-112; Coverage: 86%)
Gene names: ELOC, TCEB1
Sequence domains: Skp1 family, tetramerisation domain
von Hippel-Lindau disease tumor suppressor Chain: C
Molecule details ›
Chain: C
Length: 162 amino acids
Theoretical weight: 18.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P40337 (Residues: 54-213; Coverage: 75%)
Gene name: VHL
Sequence domains:
Bromodomain-containing protein 4 Chain: D
Molecule details ›
Chain: D
Length: 127 amino acids
Theoretical weight: 15.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60885 (Residues: 44-168; Coverage: 9%)
Gene names: BRD4, HUNK1
Sequence domains: Bromodomain

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand QIK 1 x QIK
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P3121
Unit cell:
a: 79.754Å b: 79.754Å c: 184.93Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.221 0.218 0.274
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Affinity for both sides.
Testa A. (2023)
2 more

1 mention without citation

Camphor, Artemisinin and Sumac Phytochemicals as inhibitors against COVID-19: Computational approach.
Belhassan et al. (2021)