ISDA

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, synthetic construct

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2021-02-03

Release Date:

2021-12-15

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

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Isoform 1 of PHD finger protein 1
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)
Description: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

Primary Citation

Discovery of an H3K36me3-Derived Peptidomimetic Ligand with Enhanced Affinity for Plant Homeodomain Finger Protein 1 (PHF1).

Engelberg, I.A, Liu, J, Norris-Drouin, J.L, Cholensky, S.H, Ottavi, S.A, Frye, S.V, Kutateladze, T.G, James, L.I.Show

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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Primary Citation of related structures