7LKY image
Deposition Date 2021-02-03
Release Date 2021-12-15
Last Version Date 2023-10-18
Entry Detail
PDB ID:
7LKY
Keywords:
Transcription/Transcription Inhibitor
Title:
Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.85 Å
R-Value Free:
0.28
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 1
7LKY validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Isoform 1 of PHD finger protein 1
Gene (Uniprot):PHF1
Chain IDs:A, B, C, D, E, F, G, H
Chain Length:64
Number of Molecules:8
Biological Source:Homo sapiens
UniProt ID:O43189 Pfam ID:PF18104
Polymer Type:polypeptide(L)
Molecule:Peptidomimetic inhibitor UNC6641
Chain IDs:I (auth: J), J (auth: I), K, L, M, N, O, P
Chain Length:8
Number of Molecules:8
Biological Source:synthetic construct
Ligand Molecules
DMS
ZN
Primary Citation
Discovery of an H3K36me3-Derived Peptidomimetic Ligand with Enhanced Affinity for Plant Homeodomain Finger Protein 1 (PHF1).
J.Med.Chem. 64 8510 8522 (2021)
PMID: 33999620 DOI: 10.1021/acs.jmedchem.1c00430

Abstact

Plant homeodomain finger protein 1 (PHF1) is an accessory component of the gene silencing complex polycomb repressive complex 2 and recognizes the active chromatin mark, trimethylated lysine 36 of histone H3 (H3K36me3). In addition to its role in transcriptional regulation, PHF1 has been implicated as a driver of endometrial stromal sarcoma and fibromyxoid tumors. We report the discovery and characterization of UNC6641, a peptidomimetic antagonist of the PHF1 Tudor domain which was optimized through in silico modeling and incorporation of non-natural amino acids. UNC6641 binds the PHF1 Tudor domain with a Kd value of 0.96 ± 0.03 μM while also binding the related protein PHF19 with similar potency. A crystal structure of PHF1 in complex with UNC6641, along with NMR and site-directed mutagenesis data, provided insight into the binding mechanism and requirements for binding. Additionally, UNC6641 enabled the development of a high-throughput assay to identify small molecule binders of PHF1.

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Disease

Primary Citation of related structures
7LKY