5F4P | pdb_00005f4p

HIV-1 gp120 complex with BNM-III-170

• PDB DOI: https://doi.org/10.2210/pdb5F4P/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-12-03 Released: 2016-03-30 
• Deposition Author(s): Liang, S., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.310 (Depositor), 0.317 (DCC) 
• R-Value Work: 
  0.274 (Depositor), 0.278 (DCC) 
• R-Value Observed: 
  0.275 (Depositor) 

Starting Model: experimental

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

• PubMed: 26985324 
• DOI: https://doi.org/10.1021/acsmedchemlett.5b00471
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States.
Department of Biochemistry and Molecular Biophysics and Department of Physiology and Cellular Biophysics, Columbia University , New York, New York 10032, United States.
Department of Biology, The Johns Hopkins University , Baltimore, Maryland 21218, United States.
Department of Chemistry, Bryn Mawr College , Bryn Mawr, Pennsylvania 19010, United States.
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, and Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States.
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, United States.
Department of Biochemistry and Molecular Biophysics and Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, United States; Department of Biochemistry and Molecular Biophysics and Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81.14 kDa 
• Atom Count: 5,497 
• Modeled Residue Count: 670 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C	A [auth D], B [auth A]	350	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for C6G099 (Human immunodeficiency virus type 1) Explore C6G099  Go to UniProtKB:  C6G099

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5VG	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	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 (Depositor), 0.317 (DCC) 
• R-Value Work:  0.274 (Depositor), 0.278 (DCC) 
• R-Value Observed: 0.275 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.378	α = 90
b = 127.517	β = 90
c = 192.945	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Liang, S., Hendrickson, W.A.

Revision History  

• 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