9CDV

Crystal Structure of Rhombotarget A

Summary for 9CDV

• Entry DOI: 10.2210/pdb9cdv/pdb
• Descriptor: Rhombotarget A, MAGNESIUM ION, 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (4 entities in total)
• Functional Keywords: de novo design, deep learning, membrane protein, cyclic peptide
• Biological source: Acinetobacter terrae
• Total number of polymer chains: 2
• Total formula weight: 101416.14

Authors

Bera, A.K.,Rettie, S.,Kang, A.,Bhardwaj, G. (deposition date: 2024-06-25, release date: 2025-07-02, Last modification date: 2025-12-10)

Primary citation

Rettie, S.A.,Juergens, D.,Adebomi, V.,Bueso, Y.F.,Zhao, Q.,Leveille, A.N.,Liu, A.,Bera, A.K.,Wilms, J.A.,Uffing, A.,Kang, A.,Brackenbrough, E.,Lamb, M.,Gerben, S.R.,Murray, A.,Levine, P.M.,Schneider, M.,Vasireddy, V.,Ovchinnikov, S.,Weiergraber, O.H.,Willbold, D.,Kritzer, J.A.,Mougous, J.D.,Baker, D.,DiMaio, F.,Bhardwaj, G.
Accurate de novo design of high-affinity protein-binding macrocycles using deep learning.
Nat.Chem.Biol., 21:1948-1956, 2025

PubMed Abstract: Developing macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource intensive and provide little control over binding mode. Despite progress in protein design, there are currently no robust approaches for de novo design of protein-binding macrocycles. Here we introduce RFpeptides, a denoising diffusion-based pipeline for designing macrocyclic binders against protein targets of interest. We tested 20 or fewer designed macrocycles against each of four diverse proteins and obtained binders with medium to high affinity against all targets. For one of the targets, Rhombotarget A (RbtA), we designed a high-affinity binder (K < 10 nM) despite starting from the predicted target structure. X-ray structures for macrocycle-bound myeloid cell leukemia 1, γ-aminobutyric acid type A receptor-associated protein and RbtA complexes match closely with the computational models, with a Cα root-mean-square deviation < 1.5 Å to the design models. RFpeptides provides a framework for rapid and custom design of macrocyclic peptides for diagnostic and therapeutic applications.

PubMed: 40542165
DOI: 10.1038/s41589-025-01929-w

Experimental method

X-RAY DIFFRACTION (2 Å)