Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 22.41 kDa 
• Atom Count: 1985 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

6U7P

HIV-1 wild type protease with GRL-03119A, with phenyl-boronic-acid as P2'-ligand and with a hexahydro-4H-furo-pyran as the P2-ligand

• PDB DOI: 10.2210/pdb6U7P/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: 1.13 Å
• R-Value Free: 0.141 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 

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: 10.1002/cmdc.201900508
• Primary Citation of 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 Refractory Viral Infections, National Center for Global Heath and Medicine Research Institute, Shinjuku, Tokyo, 162-8655, Japan.

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 1) Explore Q5RZ08  Go to UniProtKB:  Q5RZ08

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B4R (Subject of Investigation/LOI)	C [auth A]	{4-[{(2R,3S)-3-[({[(3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-yl]oxy}carbonyl)amino]-2-hydroxy-4-phenylbutyl}(2-methylpropyl)sulfamoyl]phenyl}boronic acid C28 H39 B N2 O9 S LVYBBLQFCOXKLU-UIPNDDLNSA-N
GOL	K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	J [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 0.141 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.491	α = 90
b = 86.097	β = 90
c = 46.086	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

• Deposited Date: 2019-09-03 
• 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