6UML image
Deposition Date 2019-10-09
Release Date 2020-04-15
Last Version Date 2024-11-06
Entry Detail
PDB ID:
6UML
Keywords:
LIGASE
Title:
Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Spodoptera frugiperda
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.58 Å
R-Value Free:
0.26
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
6UML validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA damage-binding protein 1
Gene (Uniprot):DDB1
Chain IDs:A
Chain Length:1140
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q16531 Pfam ID:PF10433, PF03178
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein cereblon
Gene (Uniprot):CRBN
Chain IDs:B (auth: C)
Chain Length:406
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96SW2 Pfam ID:PF02190, PF03226
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sal-like protein 4
Gene (Uniprot):SALL4
Chain IDs:C (auth: E)
Chain Length:28
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UJQ4 Pfam ID:PF00096
Ligand Molecules
Y70
ZN
Primary Citation
Crystal structure of the SALL4-pomalidomide-cereblon-DDB1 complex.
Nat.Struct.Mol.Biol. 27 319 322 (2020)
PMID: 32251415 DOI: 10.1038/s41594-020-0405-9

Abstact

Thalidomide-dependent degradation of the embryonic transcription factor SALL4 by the CRL4CRBN E3 ubiquitin ligase is a plausible major driver of thalidomide teratogenicity. The structure of the second zinc finger of SALL4 in complex with pomalidomide, cereblon and DDB1 reveals the molecular details of recruitment. Sequence differences and a shifted binding position relative to Ikaros offer a path to the rational design of cereblon-binding drugs with reduced teratogenic risk.

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Protein

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Disease

Primary Citation of related structures
6UML