› 4ybm

X-ray diffraction
1.46Å resolution

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

Released:
DOI: 10.2210/pdb4ybm/pdb
PDB entry 4ybm coloured by chain, front view.
PDB entry 4ybm coloured by chain, side view.
PDB entry 4ybm 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 Chains: A, B
Molecule details ›
Chains: A, B
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

4 bound ligands:
Ligand ZN 4 x ZN
Ligand GOL 4 x GOL
Ligand 4BJ 2 x 4BJ
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 37.4Å b: 79.82Å c: 131.69Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.163 0.196
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

6 mentions without citation

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations.
Aldeghi et al. (2017)
5 more