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: 22.47 kDa 
• Atom Count: 1840 
• Residue Count: 198 
• Unique protein chains: 1

5UOV

HIV-1 wild Type protease with GRL-1118A , an isophthalamide-derived P2-P3 ligand with the sulfonamide isostere as the P2' group

• DOI: 10.2210/pdb5UOV/pdb

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


• Deposited: 2017-02-01 Released: 2017-05-10 
• 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, Purdue University

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.183 
• R-Value Work: 0.152 

Literature

Design of novel HIV-1 protease inhibitors incorporating isophthalamide-derived P2-P3 ligands: Synthesis, biological evaluation and X-ray structural studies of inhibitor-HIV-1 protease complex.

Ghosh, A.K., Brindisi, M., Nyalapatla, P.R., Takayama, J., Ella-Menye, J.R., Yashchuk, S., Agniswamy, J., Wang, Y.F., Aoki, M., Amano, M., Weber, I.T., Mitsuya, H.

(2017) Bioorg Med Chem 25: 5114-5127

• PubMed: 28434781 
• DOI: 10.1016/j.bmc.2017.04.005
• Primary Citation of Related Structures:  
  5UOV, 5UPZ


• PubMed Abstract: 
  

Based upon molecular insights from the X-ray structures of inhibitor-bound HIV-1 protease complexes, we have designed a series of isophthalamide-derived inhibitors incorporating substituted pyrrolidines, piperidines and thiazolidines as P2-P3 ligands for specific interactions in the S2-S3 extended site. Compound 4b has shown an enzyme K _i of 0.025nM and antiviral IC ₅₀ of 69nM. An X-ray crystal structure of inhibitor 4b-HIV-1 protease complex was determined at 1.33Å resolution. We have also determined X-ray structure of 3b-bound HIV-1 protease at 1.27Å resolution. These structures revealed important molecular insight into the inhibitor-HIV-1 protease interactions in the active site.

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Organizational Affiliation: 

Department of Hematology, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Department of Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892, USA; Department of Refractory Viral Infection, National Center for Global Health 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 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)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8FP	A	N-[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]-3-[(2R)-2-(4-methyl-1,3-thiazol-2-yl)pyrrolidine-1-carbonyl]benzamide C37 H44 N4 O6 S2 ZHCCHBWXFODCGA-LBFZIJHGSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
8FP	Ki:  0.02500000037252903   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.183 
• R-Value Work: 0.152 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.179	α = 90
b = 86.515	β = 90
c = 45.945	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-01 
• Released Date: 2017-05-10 
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
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)
Purdue University	United States	the Purdue University Center for Cancer Research

Revision History 

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2017-10-04
  Changes: Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence