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 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acsmedchemlett.5b00471
  • Primary Citation of Related Structures:  
    5F4L, 5F4P, 5F4R, 5F4U

  • 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, 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
A, B
350Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for C6G099 (Human immunodeficiency virus 1)
Explore C6G099 
Go to UniProtKB:  C6G099
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6G099
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5VE
Query on 5VE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Structure summary