5F4U

HIV-1 gp120 complex with BNM-IV-197


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition.

Melillo, B.Liang, S.Park, J.Schon, A.Courter, J.R.LaLonde, J.M.Wendler, D.J.Princiotto, A.M.Seaman, M.S.Freire, E.Sodroski, J.Madani, N.Hendrickson, W.A.Smith, A.B.

(2016) ACS Med Chem Lett 7: 330-334

  • DOI: 10.1021/acsmedchemlett.5b00471
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The optimization, based on computational, thermodynamic, and crystallographic data, of a series of small-molecule ligands of the Phe43 cavity of the envelope glycoprotein gp120 of human immunodeficiency virus (HIV) has been achieved. Importantly, bio ...

    The optimization, based on computational, thermodynamic, and crystallographic data, of a series of small-molecule ligands of the Phe43 cavity of the envelope glycoprotein gp120 of human immunodeficiency virus (HIV) has been achieved. Importantly, biological evaluation revealed that the small-molecule CD4 mimics (4-7) inhibit HIV-1 entry into target cells with both significantly higher potency and neutralization breadth than previous congeners, while maintaining high selectivity for the target virus. Their binding mode was characterized via thermodynamic and crystallographic studies.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
A, B
350Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for C6G099 (Human immunodeficiency virus 1)
Go to UniProtKB:  C6G099
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
5VH
Query on 5VH

Download SDF File 
Download CCD File 
A, B
~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide
C22 H26 Cl F N8 O2
SEZMROBQXWBHMW-FZKQIMNGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 67.439α = 90.00
b = 128.123β = 90.00
c = 193.599γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Derived calculations, Refinement description