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Structure paper

TitleIndoline CD4-mimetic compounds mediate potent and broad HIV-1 inhibition and sensitization to antibody-dependent cellular cytotoxicity.
Journal, issue, pagesProc. Natl. Acad. Sci. USA, Vol. 120, Page e2222073120-e2222073120, Year 2023
Publish dateDec 22, 2022 (structure data deposition date)
AuthorsFritschi, C.J. / Anang, S. / Gong, Z. / Mohammadi, M. / Richard, J. / Bourassa, C. / Severino, K.T. / Richter, H. / Yang, D. / Chen, H.C. ...Fritschi, C.J. / Anang, S. / Gong, Z. / Mohammadi, M. / Richard, J. / Bourassa, C. / Severino, K.T. / Richter, H. / Yang, D. / Chen, H.C. / Chiu, T.J. / Seaman, M.S. / Madani, N. / Abrams, C. / Finzi, A. / Hendrickson, W.A. / Sodroski, J.G. / Smith III, A.B.
External linksProc. Natl. Acad. Sci. USA / PubMed:36961924
MethodsX-ray diffraction
Resolution1.88 - 2.47 Å
Structure data

PDB-8fly:
HIV-1 gp120 complex with BNM-III-170
Method: X-RAY DIFFRACTION / Resolution: 2.04 Å

PDB-8flz:
HIV-1 gp120 complex with CJF-III-049-S
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-8fm0:
HIV-1 gp120 complex with CJF-III-214
Method: X-RAY DIFFRACTION / Resolution: 2.08 Å

PDB-8fm2:
HIV-1 gp120 complex with CJF-III-289
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-8fm3:
HIV-1 gp120 complex with CJF-III-288
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-8fm4:
HIV-1 gp120 complex with CJF-IV-047
Method: X-RAY DIFFRACTION / Resolution: 2.18 Å

PDB-8fm5:
HIV-1 gp120 complex with DY-III-065
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-8fm7:
HIV-1 gp120 complex with CJF-III-192
Method: X-RAY DIFFRACTION / Resolution: 2.34 Å

PDB-8fm8:
HIV-1 gp120 complex with CJF-IV-046
Method: X-RAY DIFFRACTION / Resolution: 2.47 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-5VG:
~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide

ChemComp-HOH:
WATER

ChemComp-7IT:
N~1~-{(1R,2R,3S)-2-(carbamimidamidomethyl)-3-[(3S)-3,4-dihydroxybutyl]-5-[(methylamino)methyl]-2,3-dihydro-1H-inden-1-yl}-N~2~-(4-chloro-3-fluorophenyl)ethanediamide

ChemComp-Y1O:
methyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate

ChemComp-Y1X:
ethyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate

ChemComp-IMD:
IMIDAZOLE

ChemComp-Y26:
propyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate

ChemComp-Y2K:
2,2,2-trifluoroethyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate

ChemComp-Y2E:
3,3,3-trifluoropropyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate

ChemComp-Y2O:
benzyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate

ChemComp-Y1T:
(pentafluorophenyl)methyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate

Source
  • hiv-1 06tg.ht008 (virus)
KeywordsVIRAL PROTEIN/INHIBITOR / retrovirus / gp120 / entry inhibitor / structure-based drug design / small molecule / antiretroviral therapy / VIRAL PROTEIN-INHIBITOR complex

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