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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.54 kDa 
• Atom Count: 2023 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

6CDJ

HIV-1 wild type protease with GRL-03314A, 6-5-5-ring fused umbrella-like tetrahydropyranofuran as the P2-ligand, a cyclopropylaminobenzothiazole as the P2'-ligand and 3,5-difluorophenylmethyl as the P1-ligand

• PDB DOI: 10.2210/pdb6CDJ/pdb

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


• Deposited: 2018-02-08 Released: 2018-05-30 
• 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), National Institutes of Health/National Cancer Institute (NIH/NCI), Ministry of Education, Culture, Sports, Science and Technology (Japan), Ministry of Health, Welfare, and Labor

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 0.173 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 

Literature

Design and Synthesis of Highly Potent HIV-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems as Novel P2 Ligands: Structure-Activity Studies, Biological and X-ray Structural Analysis.

Ghosh, A.K., R Nyalapatla, P., Kovela, S., Rao, K.V., Brindisi, M., Osswald, H.L., Amano, M., Aoki, M., Agniswamy, J., Wang, Y.F., Weber, I.T., Mitsuya, H.

(2018) J Med Chem 61: 4561-4577

• PubMed: 29763303 
• DOI: 10.1021/acs.jmedchem.8b00298
• Primary Citation of Related Structures:  
  6CDJ, 6CDL


• PubMed Abstract: 
  

The design, synthesis, and biological evaluation of a new class of HIV-1 protease inhibitors containing stereochemically defined fused tricyclic polyethers as the P2 ligands and a variety of sulfonamide derivatives as the P2' ligands are described. A number of ring sizes and various substituent effects were investigated to enhance the ligand-backbone interactions in the protease active site. Inhibitors 5c and 5d containing this unprecedented fused 6-5-5 ring system as the P2 ligand, an aminobenzothiazole as the P2' ligand, and a difluorophenylmethyl as the P1 ligand exhibited exceptional enzyme inhibitory potency and maintained excellent antiviral activity against a panel of highly multidrug-resistant HIV-1 variants. The umbrella-like P2 ligand for these inhibitors has been synthesized efficiently in an optically active form using a Pauson-Khand cyclization reaction as the key step. The racemic alcohols were resolved efficiently using a lipase catalyzed enzymatic resolution. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease revealed extensive interactions with the backbone atoms of HIV-1 protease and provided molecular insight into the binding properties of these new inhibitors.

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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	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: pol
UniProt
Find proteins for Q5RZ08 (Human immunodeficiency virus 1) Explore Q5RZ08  Go to UniProtKB:  Q5RZ08

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GR8	C [auth A]	(2aS,4R,4aS,7aS,7bS)-octahydro-2H-1,7-dioxacyclopenta[cd]inden-4-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate C34 H42 F2 N4 O7 S2 NIZKZMLJMFCQSW-FQOBIZQLSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	I [auth B], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	E [auth A], G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GR8	BindingDB:  6CDJ	Ki: 2.00e-3 (nM) from 1 assay(s)
	Binding MOAD:  6CDJ	Ki: 2.00e-3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 0.173 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.959	α = 90
b = 86.077	β = 90
c = 46.157	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: 2018-02-08 
• Released Date: 2018-05-30 
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
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)

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2018-06-06
  Changes: Data collection, Database references
• Version 1.2: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence