8FM5

HIV-1 gp120 complex with DY-III-065


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Indoline CD4-mimetic compounds mediate potent and broad HIV-1 inhibition and sensitization to antibody-dependent cellular cytotoxicity.

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.

(2023) Proc Natl Acad Sci U S A 120: e2222073120-e2222073120

  • DOI: https://doi.org/10.1073/pnas.2222073120
  • Primary Citation of Related Structures:  
    8FLY, 8FLZ, 8FM0, 8FM2, 8FM3, 8FM4, 8FM5, 8FM7, 8FM8

  • PubMed Abstract: 

    Binding to the host cell receptors, CD4 and CCR5/CXCR4, triggers large-scale conformational changes in the HIV-1 envelope glycoprotein (Env) trimer [(gp120/gp41) 3 ] that promote virus entry into the cell. CD4-mimetic compounds (CD4mcs) comprise small organic molecules that bind in the highly conserved CD4-binding site of gp120 and prematurely induce inactivating Env conformational changes, including shedding of gp120 from the Env trimer. By inducing more "open," antibody-susceptible Env conformations, CD4mcs also sensitize HIV-1 virions to neutralization by antibodies and infected cells to antibody-dependent cellular cytotoxicity (ADCC). Here, we report the design, synthesis, and evaluation of novel CD4mcs based on an indoline scaffold. Compared with our current lead indane scaffold CD4mc, BNM-III-170, several indoline CD4mcs exhibit increased potency and breadth against HIV-1 variants from different geographic clades. Viruses that were selected for resistance to the lead indane CD4mc, BNM-III-170, are susceptible to inhibition by the indoline CD4mcs. The indoline CD4mcs also potently sensitize HIV-1-infected cells to ADCC mediated by plasma from HIV-1-infected individuals. Crystal structures indicate that the indoline CD4mcs gain potency compared to the indane CD4mcs through more favorable π-π overlap from the indoline pose and by making favorable contacts with the vestibule of the CD4-binding pocket on gp120. The rational design of indoline CD4mcs thus holds promise for further improvements in antiviral activity, potentially contributing to efforts to treat and prevent HIV-1 infection.


  • Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A [auth D],
B [auth A],
C,
D [auth B]
358HIV-1 06TG.HT008Mutation(s): 0 
UniProt
Find proteins for C6G099 (Human immunodeficiency virus type 1)
Explore C6G099 
Go to UniProtKB:  C6G099
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6G099
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y2E (Subject of Investigation/LOI)
Query on Y2E

Download Ideal Coordinates CCD File 
HA [auth B],
K [auth D],
R [auth A],
Z [auth C]
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
C24 H26 Cl F4 N7 O4
PUALTKTUZNGQRL-MOPGFXCFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth B]
CA [auth B]
DA [auth B]
E [auth D]
AA [auth C],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth D],
EA [auth B],
F [auth D],
FA [auth B],
G [auth D],
GA [auth B],
H [auth D],
I [auth D],
J [auth D],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
S [auth A],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.52α = 90
b = 121.66β = 90
c = 195.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesAI150471-25 8117

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary