7RSY

HIV-1 gp120 complex with CJF-III-049-R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of gp120 Residue His105 as a Novel Target for HIV-1 Neutralization by Small-Molecule CD4-Mimics.

Fritschi, C.J.Liang, S.Mohammadi, M.Anang, S.Moraca, F.Chen, J.Madani, N.Sodroski, J.G.Abrams, C.F.Hendrickson, W.A.Smith 3rd, A.B.

(2021) ACS Med Chem Lett 12: 1824-1831

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00437
  • Primary Citation of Related Structures:  
    7RSX, 7RSY, 7RSZ

  • PubMed Abstract: 

    The design and synthesis of butyl chain derivatives at the indane ring 3-position of our lead CD4-mimetic compound BNM-III-170 that inhibits human immunodeficiency virus (HIV-1) infection are reported. Optimization efforts were guided by crystallographic and computational analysis of the small-molecule ligands of the Phe43 cavity of the envelope glycoprotein gp120. Biological evaluation of 11 - 21 revealed that members of this series of CD4-mimetic compounds are able to inhibit HIV-1 viral entry into target cells more potently and with greater breadth compared to BNM-III-170. Crystallographic analysis of the binding pocket of 14 , 16 , and 17 revealed a novel hydrogen bonding interaction between His105 and a primary hydroxyl group on the butyl side chain. Further optimization of this interaction with the His105 residue holds the promise of more potent CD4-mimetic compounds.


  • Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 gp120 Clade C1086
A, B, C, D
362Human immunodeficiency virus 1Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7IW (Subject of Investigation/LOI)
Query on 7IW

Download Ideal Coordinates CCD File 
FA [auth D],
L [auth A],
S [auth B],
Y [auth C]
N~1~-{(1R,2R,3S)-2-(carbamimidamidomethyl)-3-[(3R)-3,4-dihydroxybutyl]-5-[(methylamino)methyl]-2,3-dihydro-1H-inden-1-yl}-N~2~-(4-chloro-3-fluorophenyl)ethanediamide
C25 H32 Cl F N6 O4
FZJJRAXEHQBZEC-GDVTWYKTSA-N
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.577α = 90
b = 120.754β = 90
c = 195.277γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM116799

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary