5F4L

HIV-1 gp120 complex with JP-III-048


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

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:  
    5F4U, 5F4L, 5F4P, 5F4R

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade CA, B350Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for C6G099 (Human immunodeficiency virus 1)
Explore C6G099 
Go to UniProtKB:  C6G099
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5VE
Query on 5VE

Download CCD File 
A, B
~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide
C21 H24 Cl F N6 O2
XFJPCFZRCFHOOP-FZKQIMNGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.159α = 90
b = 127.806β = 90
c = 192.47γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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