5F4P

HIV-1 gp120 complex with BNM-III-170

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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 CA [auth D],
B [auth A]		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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5VG
Query on 5VG
Download Ideal Coordinates CCD File 
I [auth D],
J [auth A]		~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide
C21 H24 Cl F N6 O2
ZUJVWZRAMJMXLF-FZKQIMNGSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
C [auth D]
D
E [auth D]
F [auth D]
G [auth D]
C [auth D],
D,
E [auth D],
F [auth D],
G [auth D],
H [auth D],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.378α = 90
b = 127.517β = 90
c = 192.945γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.3: 2024-11-13
    Changes: Structure summary