6U7O | pdb_00006u7o

HIV-1 wild type protease with GRL-00819A, with phenyl-boronic-acid as P2'-ligand and with a 6-5-5-ring fused crown-like tetrahydropyranofuran as the P2-ligand

• PDB DOI: https://doi.org/10.2210/pdb6U7O/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-09-03 Released: 2019-10-09 
• Deposition Author(s): Wang, Y.-F., Kneller, D.W., Weber, I.T.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 
  0.177 (Depositor), 0.142 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Potent HIV-1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein-Ligand X-ray Structural Studies.

Ghosh, A.K., Xia, Z., Kovela, S., Robinson, W.L., Johnson, M.E., Kneller, D.W., Wang, Y.F., Aoki, M., Takamatsu, Y., Weber, I.T., Mitsuya, H.

(2019) ChemMedChem 14: 1863-1872

• PubMed: 31549492 
• DOI: https://doi.org/10.1002/cmdc.201900508
• Primary Citation Related Structures: 
  6U7O, 6U7P


• PubMed Abstract: 
  

  We report the synthesis and biological evaluation of phenylcarboxylic acid and phenylboronic acid containing HIV-1 protease inhibitors and their functional effect on enzyme inhibition and antiviral activity in MT-2 cell lines. Inhibitors bearing bis-THF ligand as P2 ligand and phenylcarboxylic acids and carboxamide as the P2' ligands, showed very potent HIV-1 protease inhibitory activity. However, carboxylic acid containing inhibitors showed very poor antiviral activity relative to carboxamide-derived inhibitors which showed good antiviral IC ₅₀ value. Boronic acid derived inhibitor with bis-THF as the P2 ligand showed very potent enzyme inhibitory activity, but it showed lower antiviral activity than darunavir in the same assay. Boronic acid containing inhibitor with a P2-Crn-THF ligand also showed potent enzyme K _i but significantly decreased antiviral activity. We have evaluated antiviral activity against a panel of highly drug-resistant HIV-1 variants. One of the inhibitors maintained good antiviral activity against HIV _DRV ^R _P20 and HIV _DRV ^R _P30 viruses. We have determined high resolution X-ray structures of two synthetic inhibitors bound to HIV-1 protease and obtained molecular insight into the ligand-binding site interactions.

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Organizational Affiliation: 
• Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA, 30303, USA.
Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA.
Department of Refractory Viral Infections, National Center for Global Heath and Medicine Research Institute, Shinjuku, Tokyo, 162-8655, Japan.
Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 22.39 kDa 
• Atom Count: 1,944 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: pol
UniProt
Find proteins for Q5RZ08 (Human immunodeficiency virus type 1) Explore Q5RZ08  Go to UniProtKB:  Q5RZ08

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q1D (Subject of Investigation/LOI)	H [auth B]	{4-[{(2R,3S)-3-[({[(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl]oxy}carbonyl)amino]-2-hydroxy-4-phenylbutyl}(2-methylpropyl)sulfamoyl]phenyl}boronic acid C29 H39 B N2 O9 S QIKRDCAMSNJRAO-HGKZDDSVSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	F [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	D [auth A], E [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.177 (Depositor), 0.142 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.145 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.921	α = 90
b = 86.479	β = 90
c = 45.875	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Wang, Y.-F., Kneller, D.W., Weber, I.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	AI150466
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	AI150461

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description