› 8ogb

X-ray diffraction
2.27Å resolution

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 8

Released:
DOI: 10.2210/pdb8ogb/pdb
PDB entry 8ogb coloured by chain, front view.
PDB entry 8ogb coloured by chain, side view.
PDB entry 8ogb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of New Binders for DCAF1, an Emerging Ligase Target in the Targeted Protein Degradation Field.
Vulpetti A, Holzer P, Schmiedeberg N, Imbach-Weese P, Pissot-Soldermann C, Hollingworth GJ, Radimerski T, Thoma CR, Stachyra TM, Wojtynek M, Maschlej M, Chau S, Schuffenhauer A, Fernández C, Schröder M, Renatus M
ACS Med Chem Lett 14 949-954 (2023)
PMID: 37465299

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195228 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DDB1- and CUL4-associated factor 1 Chain: A
Molecule details ›
Chain: A
Length: 367 amino acids
Theoretical weight: 41.76 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9Y4B6 (Residues: 1039-1401; Coverage: 24%)
Gene names: DCAF1, KIAA0800, RIP, VPRBP

Ligands and Environments

3 bound ligands:
Ligand EDO 1 x EDO
Ligand VN5 1 x VN5
Ligand DMS 2 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P6122
Unit cell:
a: 85.018Å b: 85.018Å c: 219.36Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.17 0.168 0.212
Expression system: Spodoptera frugiperda

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Citations

1 citations in other articles

DCAF1-based PROTACs with activity against clinically validated targets overcoming intrinsic- and acquired-degrader resistance.
Schröder et al. (2024)