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Structure paper

TitleAccurate de novo design of high-affinity protein-binding macrocycles using deep learning.
Journal, issue, pagesNat. Chem. Biol., Vol. 21, Page 1948-1956, Year 2025
Publish dateJun 25, 2024 (structure data deposition date)
AuthorsRettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. ...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.
External linksNat. Chem. Biol. / PubMed:40542165
MethodsX-ray diffraction
Resolution1.5 - 2.61 Å
Structure data

PDB-9cdt:
Crystal Structure of MCL-1-Peptide Complex
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-9cdu:
Crystal Structure of Rhombotarget A-peptide Complex
Method: X-RAY DIFFRACTION / Resolution: 2.61 Å

PDB-9cdv:
Crystal Structure of Rhombotarget A
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-9hgc:
Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8
Method: X-RAY DIFFRACTION / Resolution: 2.52 Å

PDB-9hgd:
Crystal structure of human GABARAP in complex with cyclic peptide GAB_D23
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

ChemComp-MG:
Unknown entry

ChemComp-BTB:
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-SO4:
SULFATE ION

ChemComp-GOL:
GLYCEROL

ChemComp-CL:
Unknown entry

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-MES:
2-(N-MORPHOLINO)-ETHANESULFONIC ACID / pH buffer*YM

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

Source
  • homo sapiens (human)
  • synthetic construct (others)
  • acinetobacter terrae (bacteria)
KeywordsAPOPTOSIS / De novo design / deep learning / macro cycle / MCL-1 / apotosis regulator / MEMBRANE PROTEIN / Cyclic peptide / PROTEIN BINDING / autophagy-related protein / GABARAPL1 / inhibitor / GABARAP

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