Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 22.23 kDa 
• Atom Count: 1856 
• Residue Count: 198 
• Unique protein chains: 1

5BRY

HIV-1 wild Type protease with GRL-011-11A (a methylamine bis-Tetrahydrofuran P2-Ligand, sulfonamide isostere derivate)

• DOI: 10.2210/pdb5BRY/pdb

• Classification: HYDROLASE/HYDROLASE Inhibitor
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-06-01 Released: 2015-09-09 
• 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), Department of Energy (DOE, United States), National Institutes of Health/National Cancer Institute (NIH/NCI), the Ministry of Education, Culture, Sports, Science, and Technology, Ministry of Health, Welfare, and Labor

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.205 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Design of HIV-1 Protease Inhibitors with Amino-bis-tetrahydrofuran Derivatives as P2-Ligands to Enhance Backbone-Binding Interactions: Synthesis, Biological Evaluation, and Protein-Ligand X-ray Studies.

Ghosh, A.K., Martyr, C.D., Osswald, H.L., Sheri, V.R., Kassekert, L.A., Chen, S., Agniswamy, J., Wang, Y.F., Hayashi, H., Aoki, M., Weber, I.T., Mitsuya, H.

(2015) J Med Chem 58: 6994-7006

• PubMed: 26306007 
• DOI: 10.1021/acs.jmedchem.5b00900
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Structure-based design, synthesis, and biological evaluation of a series of very potent HIV-1 protease inhibitors are described. In an effort to improve backbone ligand-binding site interactions, we have incorporated basic-amines at the C4 position of the bis-tetrahydrofuran (bis-THF) ring. We speculated that these substituents would make hydrogen bonding interactions in the flap region of HIV-1 protease. Synthesis of these inhibitors was performed diastereoselectively. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 25f, 25i, and 25j were evaluated against a number of highly-PI-resistant HIV-1 strains, and they exhibited improved antiviral activity over darunavir. Two high resolution X-ray structures of 25f- and 25g-bound HIV-1 protease revealed unique hydrogen bonding interactions with the backbone carbonyl group of Gly48 as well as with the backbone NH of Gly48 in the flap region of the enzyme active site. These ligand-binding site interactions are possibly responsible for their potent activity.

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Organizational Affiliation: 

Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protease	A, B	99	Human immunodeficiency virus type 1 BH10	Mutation(s): 5  Gene Names: gag-pol EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4UY	B	(3R,3aS,4R,6aR)-4-(methylamino)hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate C29 H41 N3 O8 S RTQZESJLDDKIAO-HJCZHRQASA-N
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4UY	Ki:  0.001500000013038516   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.205 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.841	α = 90
b = 86.325	β = 90
c = 45.63	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-01 
• Released Date: 2015-09-09 
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
Department of Energy (DOE, United States)	United States	W-31-109-Eng-38
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	the Intramural Research Program of the Center for Cancer Research
the Ministry of Education, Culture, Sports, Science, and Technology	Japan	a Grant-in-Aid for Scientific Research (Priority Areas)
the Ministry of Education, Culture, Sports, Science, and Technology	Japan	the Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo)
Ministry of Health, Welfare, and Labor	Japan	a Grant for Promotion of AIDS Research

Revision History 

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-09-23
  Changes: Data collection, Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence