Biological Assembly 1  

 3D View: Structure | 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.33 kDa 
• Atom Count: 1904 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

6B4N

a hydroxymethyl functionality at the 4-position of the 2-phenyloxazole moiety of HIV-1 protease inhibitors involving the P2' ligands

• DOI: 10.2210/pdb6B4N/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-09-27 Released: 2017-11-22 
• Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), Ministry of Education, Culture, Sports, Science and Technology (Japan), Ministry of Health, Welfare, and Labor

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.196 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Literature

Design, Synthesis, Biological Evaluation, and X-ray Studies of HIV-1 Protease Inhibitors with Modified P2' Ligands of Darunavir.

Ghosh, A.K., Fyvie, W.S., Brindisi, M., Steffey, M., Agniswamy, J., Wang, Y.F., Aoki, M., Amano, M., Weber, I.T., Mitsuya, H.

(2017) ChemMedChem 12: 1942-1952

• PubMed: 29110408 
• DOI: 10.1002/cmdc.201700614
• Primary Citation of Related Structures:  
  6B4N


• PubMed Abstract: 
  

The structure-based design, synthesis, and biological evaluation of a series of nonpeptidic HIV-1 protease inhibitors with rationally designed P2' ligands are described. The inhibitors are designed to enhance backbone binding interactions, particularly at the S2' subsite. Synthesis of inhibitors was carried out efficiently. The stereochemistry of alcohol functionalities of the P2' ligands was set by asymmetric reduction of the corresponding ketone using (R,R)- or (S,S)-Noyori catalysts. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 3g and 3h showed enzyme K _i values of 27.9 and 49.7 pm and antiviral activity of 6.2 and 3.9 nm, respectively. These inhibitors also remained quite potent against darunavir-resistant HIV-1 variants. An X-ray structure of inhibitor 3g in complex with HIV-1 protease revealed key interactions in the S2' subsite.

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Organizational Affiliation: 

Center for Clinical Sciences, National Center for Global Heath and Medicine, 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 EC: 2.7.7.49 (UniProt), 3.1.13.2 (UniProt), 3.1.26.13 (UniProt)
UniProt
Find proteins for Q72498 (Human immunodeficiency virus 1) Explore Q72498  Go to UniProtKB:  Q72498

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G53 (Subject of Investigation/LOI)	C [auth A]	methyl 2-{4-[{(2R,3S)-3-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-2-hydroxy-4-phenylbutyl}(2-methylpropyl)sulfamoyl]phenyl}-1,3-oxazole-4-carboxylate C32 H39 N3 O10 S JQOKXPZOASVDIX-FHDJBOIYSA-N
CL	E [auth A], G [auth B], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
G53	Binding MOAD:  6B4N	Ki: 0.03 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.196 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.99	α = 90
b = 86.399	β = 90
c = 45.76	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-09-27 
• Released Date: 2017-11-22 
Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM53386
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM62920
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	National Institutes of Health/National Center for Research Resources
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	a Grant-in-Aid for Scientific Research (Priority Areas)
Ministry of Health, Welfare, and Labor	Japan	a Grant for Promotion of AIDS Research
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	the Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo)

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Author supporting evidence
• Version 1.2: 2017-12-20
  Changes: Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence