8Z6C

Crystal structure of HDGFRP2 PWWP domain in complex with 4-(4-bromo-1H-pyrazol-3-yl) pyridine

This is a non-PDB format compatible entry.

Summary for 8Z6C

• Entry DOI: 10.2210/pdb8z6c/pdb
• Descriptor: Hepatoma-derived growth factor-related protein 2, 4-(4-bromanyl-1~{H}-pyrazol-3-yl)pyridine, SULFATE ION, ... (4 entities in total)
• Functional Keywords: hepatoma-derived growth factor-related protein 2, pwwp domain, hit, signaling protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 3
• Total formula weight: 33124.04

Authors

Wei, X.,Ruan, K. (deposition date: 2024-04-19, release date: 2025-04-23, Last modification date: 2025-12-24)

Primary citation

Wei, X.,Li, S.,Li, Z.,Wang, L.,Fan, W.,Ruan, K.,Gao, J.
Fragment-based discovery of small molecule inhibitors of the HDGFRP2 PWWP domain.
Febs Lett., 598:2533-2543, 2024

PubMed Abstract: The PWWP domain of hepatoma-derived growth factor-related protein 2 (HDGFRP2) recognizes methylated histones to initiate the recruitment of homologous recombination repair proteins to damaged silent genes. The combined depletion of HDGFRP2 and its paralog PSIP1 effectively impedes the onset and progression of diffuse intrinsic pontine glioma (DIPG). Here, we discovered varenicline and 4-(4-bromo-1H-pyrazol-3-yl) pyridine (BPP) as inhibitors of the HDGFRP2 PWWP domain through a fragment-based screening method. The complex crystal structures reveal that both Varenicline and BPP engage with the aromatic cage of the HDGFRP2 PWWP domain, albeit via unique binding mechanisms. Notably, BPP represents the first single-digit micromolar inhibitor of the HDGFRP2 PWWP domain with a high ligand efficiency. As a dual inhibitor targeting both HDGFRP2 and PSIP1 PWWP domains, BPP offers an exceptional foundation for further optimization into a chemical tool to dissect the synergetic function of HDGFRP2 and PSIP1 in DIPG pathogenesis.

PubMed: 39031937
DOI: 10.1002/1873-3468.14981

Experimental method

X-RAY DIFFRACTION (1.93 Å)