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: 22.20 kDa 
• Atom Count: 1751 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

5JFP

HIV-1 wild Type protease with GRL-097-13A (a Adamantane P1-Ligand with bis-THF in P2 and isobutylamine in P1')

• PDB DOI: 10.2210/pdb5JFP/pdb

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


• Deposited: 2016-04-19 Released: 2016-09-21 
• 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), Ministry of Education, Culture, Sports, Science and Technology (Japan), Ministry of Health, Welfare, and Labor

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.237 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Probing Lipophilic Adamantyl Group as the P1-Ligand for HIV-1 Protease Inhibitors: Design, Synthesis, Protein X-ray Structural Studies, and Biological Evaluation.

Ghosh, A.K., Osswald, H.L., Glauninger, K., Agniswamy, J., Wang, Y.F., Hayashi, H., Aoki, M., Weber, I.T., Mitsuya, H.

(2016) J Med Chem 59: 6826-6837

• PubMed: 27389367 
• DOI: 10.1021/acs.jmedchem.6b00639
• Primary Citation of Related Structures:  
  5JFP, 5JFU, 5JG1


• PubMed Abstract: 
  

A series of potent HIV-1 protease inhibitors with a lipophilic adamantyl P1 ligand have been designed, synthesized, and evaluated. We have developed an enantioselective synthesis of adamantane-derived hydroxyethylamine isosteres utilizing Sharpless asymmetric epoxidation as the key step. Various inhibitors incorporating P1-adamantylmethyl in combination with P2 ligands such as 3-(R)-THF, 3-(S)-THF, bis-THF, and THF-THP were examined. The S1' pocket was also probed with phenyl and phenylmethyl ligands. Inhibitor 15d, with an isobutyl P1' ligand and a bis-THF P2 ligand, proved to be the most potent of the series. The cLogP value of inhibitor 15d is improved compared to inhibitor 2 with a phenylmethyl P1-ligand. X-ray structural studies of 15d, 15h, and 15i with HIV-1 protease complexes revealed molecular insight into the inhibitor-protein interaction.

---

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	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: pol EC: 3.4.23.16 (UniProt), 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)
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
6KK	E [auth B]	(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]butan-2-yl}carbamate C32 H48 N2 O8 S ZMOFGDZIKIFMEU-JTPLMOPKSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6KK	Binding MOAD:  5JFP	Ki: 0.48 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.237 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.1	α = 90
b = 86.14	β = 90
c = 45.949	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-04-19 
• Released Date: 2016-09-21 
Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.

---

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
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	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: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence