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: 22.31 kDa 
• Atom Count: 1702 
• Residue Count: 198 
• Unique protein chains: 1

5TYS

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-142

• DOI: 10.2210/pdb5TYS/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-21 Released: 2017-10-18 
• Deposition Author(s): Yedidi, R.S., Hayashi, H., Aoki, M., Das, D., Ghosh, A.K., Mitsuya, H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.237 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency.

Aoki, M., Hayashi, H., Rao, K.V., Das, D., Higashi-Kuwata, N., Bulut, H., Aoki-Ogata, H., Takamatsu, Y., Yedidi, R.S., Davis, D.A., Hattori, S.I., Nishida, N., Hasegawa, K., Takamune, N., Nyalapatla, P.R., Osswald, H.L., Jono, H., Saito, H., Yarchoan, R., Misumi, S., Ghosh, A.K., Mitsuya, H.

(2017) Elife 6

• PubMed: 29039736 
• DOI: 10.7554/eLife.28020
• Primary Citation of Related Structures:  
  5TYS, 5TYR


• PubMed Abstract: 
  

Antiretroviral therapy for HIV-1 infection/AIDS has significantly extended the life expectancy of HIV-1-infected individuals and reduced HIV-1 transmission at very high rates. However, certain individuals who initially achieve viral suppression to undetectable levels may eventually suffer treatment failure mainly due to adverse effects and the emergence of drug-resistant HIV-1 variants. Here, we report GRL-142, a novel HIV-1 protease inhibitor containing an unprecedented 6-5-5-ring-fused crown-like tetrahydropyranofuran, which has extremely potent activity against all HIV-1 strains examined with IC ₅₀ values of attomolar-to-picomolar concentrations, virtually no effects on cellular growth, extremely high genetic barrier against the emergence of drug-resistant variants, and favorable intracellular and central nervous system penetration. GRL-142 forms optimum polar, van der Waals, and halogen bond interactions with HIV-1 protease and strongly blocks protease dimerization, demonstrating that combined multiple optimizing elements significantly enhance molecular and atomic interactions with a target protein and generate unprecedentedly potent and practically favorable agents.

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Organizational Affiliation: 

National Center for Global Health and Medicine Research Institute, Tokyo, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: pol
Find proteins for G0X8E8 (Human immunodeficiency virus 1) Explore G0X8E8  Go to UniProtKB:  G0X8E8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7OA	A	(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate C33 H40 F2 N4 O7 S2 ARWGTMGGJGADTI-VFGYXJDYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
7OA	IC50:  0.01899999938905239   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.237 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.131	α = 90
b = 63.131	β = 90
c = 82.229	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-11-21 
• Released Date: 2017-10-18 
Deposition Author(s): Yedidi, R.S., Hayashi, H., Aoki, M., Das, D., Ghosh, A.K., Mitsuya, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History 

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence