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: 22.44 kDa 
• Atom Count: 2037 
• Residue Count: 198 
• Unique protein chains: 1

4ZIP

HIV-1 wild Type protease with GRL-0648A (a isophthalamide-derived P2-Ligand)

• DOI: 10.2210/pdb4ZIP/pdb

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


• Deposited: 2015-04-28 Released: 2015-07-15 
• 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), the Intramural Research Program of the Center for Cancer Research, National Institutes of Health/National Cancer Institute (NIH/NCI), Grant-in-Aid for Scientific Research (Priority Areas) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (Monbu Kagakusho), Ministry of Health, Welfare, and Labor

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 0.154 
• R-Value Work: 0.130 
• R-Value Observed: 0.131 

Literature

Structure-based design, synthesis, X-ray studies, and biological evaluation of novel HIV-1 protease inhibitors containing isophthalamide-derived P2-ligands.

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

(2015) Bioorg Med Chem Lett 25: 4903-4909

• PubMed: 26096678 
• DOI: 10.1016/j.bmcl.2015.05.052
• Primary Citation of Related Structures:  
  4ZIP


• PubMed Abstract: 
  

We describe the design, synthesis and biological evaluation of a series of novel HIV-1 protease inhibitors bearing isophthalamide derivatives as the P2-P3 ligands. We have investigated a range of acyclic and heterocyclic amides as the extended P2-P3 ligands. These inhibitors displayed good to excellent HIV-1 protease inhibitory activity. Also, a number of inhibitors showed very good antiviral activity in MT cells. Compound 5n has shown an enzyme Ki of 0.17 nM and antiviral IC50 of 14 nM. An X-ray crystal structure of inhibitor 5o-bound to HIV-1 protease was determined at 1.11Å resolution. This structure revealed important molecular insight into the inhibitor-HIV-1 protease interactions in the active site.

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Organizational Affiliation: 

Departments of Hematology and 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; Center for Clinical Sciences, National Center for Global Health 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 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G64	B	N-[(2,5-dimethyl-1,3-oxazol-4-yl)methyl]-N'-[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]-N,5-dimethylbenzene-1,3-dicarboxamide C37 H46 N4 O7 S VYTQZAGDUBREEP-QWOOXDRHSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-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 %)
G64	Ki:  0.20000000298023224   nM  BindingDB
G64	Ki:  0.20999999344348907   nM  BindingDB
G64	IC50:  30   nM  BindingDB
G64	Ki:  0.20999999344348907   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 0.154 
• R-Value Work: 0.130 
• R-Value Observed: 0.131 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58	α = 90
b = 86.28	β = 90
c = 46.13	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-04-28 
• Released Date: 2015-07-15 
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	GM62920
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM53386
the Intramural Research Program of the Center for Cancer Research	United States	--
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--
Grant-in-Aid for Scientific Research (Priority Areas) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (Monbu Kagakusho)	Japan	Grant-in-Aid for Scientific Research (Priority Areas)
Ministry of Health, Welfare, and Labor	Japan	Grant for Promotion of AIDS Research
Ministry of Health, Welfare, and Labor	Japan	the Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo) of Monbu-Kagakusho

Revision History 

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2015-10-28
  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