› 4ybs

X-ray diffraction
1.83Å resolution

Crystal structure of TRIM24 PHD-bromodomain complexed with N-{1,3-dimethyl-6-[3-(2-methylpropoxy)phenoxy]-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-1,2-dimethyl-1H-imidazole-4-sulfonamide (7g)

Released:
DOI: 10.2210/pdb4ybs/pdb
PDB entry 4ybs coloured by chain, front view.
PDB entry 4ybs coloured by chain, side view.
PDB entry 4ybs coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Guided Design of IACS-9571, a Selective High-Affinity Dual TRIM24-BRPF1 Bromodomain Inhibitor.
Palmer WS, Poncet-Montange G, Liu G, Petrocchi A, Reyna N, Subramanian G, Theroff J, Yau A, Kost-Alimova M, Bardenhagen JP, Leo E, Shepard HE, Tieu TN, Shi X, Zhan Y, Zhao S, Barton MC, Draetta G, Toniatti C, Jones P, Geck Do M, Andersen JN
J Med Chem 59 1440-54 (2016)
PMID: 26061247

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127337 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Transcription intermediary factor 1-alpha Chain: A
Molecule details ›
Chain: A
Length: 184 amino acids
Theoretical weight: 21.32 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O15164 (Residues: 824-1006; Coverage: 17%)
Gene names: RNF82, TIF1, TIF1A, TRIM24
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand 4BK 1 x 4BK
Ligand DMS 1 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2
Unit cell:
a: 90.735Å b: 36.238Å c: 65.935Å
α: 90° β: 111.56° γ: 90°
R-values:
R R work R free
0.17 0.167 0.231
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

30 review citations

Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials.
Cheng et al. (2019)
29 more

2 mentions without citation

Structure-Guided Design of IACS-9571, a Selective High-Affinity Dual TRIM24-BRPF1 Bromodomain Inhibitor.
Palmer et al. (2016)
1 more