Biological Assembly 1  

 3D View: Structure | 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: 24.75 kDa 
• Atom Count: 1972 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

3I6O

Crystal structure of wild type HIV-1 protease with macrocyclic inhibitor GRL-0216A

• DOI: 10.2210/pdb3I6O/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus type 1 (BRU ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-07-07 Released: 2009-09-29 
• Deposition Author(s): Chumanevich, A.A., Wang, Y.-F., Kovalevsky, A.Y., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 0.196 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Literature

Design, Synthesis, Protein-Ligand X-ray Structure, and Biological Evaluation of a Series of Novel Macrocyclic Human Immunodeficiency Virus-1 Protease Inhibitors to Combat Drug Resistance.

Ghosh, A.K., Kulkarni, S., Anderson, D.D., Hong, L., Baldridge, A., Wang, Y.F., Chumanevich, A.A., Kovalevsky, A.Y., Tojo, Y., Amano, M., Koh, Y., Tang, J., Weber, I.T., Mitsuya, H.

(2009) J Med Chem 52: 7689-7705

• PubMed: 19746963 
• DOI: 10.1021/jm900695w
• Primary Citation of Related Structures:  
  3I6O, 3I7E


• PubMed Abstract: 
  

The structure-based design, synthesis, and biological evaluation of a series of nonpeptidic macrocyclic HIV protease inhibitors are described. The inhibitors are designed to effectively fill in the hydrophobic pocket in the S1'-S2' subsites and retain all major hydrogen bonding interactions with the protein backbone similar to darunavir (1) or inhibitor 2. The ring size, the effect of methyl substitution, and unsaturation within the macrocyclic ring structure were assessed. In general, cyclic inhibitors were significantly more potent than their acyclic homologues, saturated rings were less active than their unsaturated analogues and a preference for 10- and 13-membered macrocylic rings was revealed. The addition of methyl substituents resulted in a reduction of potency. Both inhibitors 14b and 14c exhibited marked enzyme inhibitory and antiviral activity, and they exerted potent activity against multidrug-resistant HIV-1 variants. Protein-ligand X-ray structures of inhibitors 2 and 14c provided critical molecular insights into the ligand-binding site interactions.

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Organizational Affiliation: 

Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus type 1 (BRU ISOLATE)	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)
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GR6 (Subject of Investigation/LOI)	Y [auth B]	(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-1-benzyl-2-hydroxy-3-[(7E)-13-methoxy-1,1-dioxido-3,4,5,6,9,10-hexahydro-2H-11,1,2-benzoxathiazacyclotridecin-2-yl]propyl}carbamate C32 H42 N2 O9 S ZQJBDIZBNGQJDT-JZAADHNPSA-N
IOD	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	L [auth A], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GR6	Binding MOAD:  3I6O	Ki: 0.05 (nM) from 1 assay(s)
	BindingDB:  3I6O	Ki: 0.06 (nM) from 1 assay(s)
		EC50: 7 (nM) from 1 assay(s)
	PDBBind:  3I6O	Ki: 0.05 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 0.196 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.764	α = 90
b = 86.328	β = 90
c = 45.976	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2009-07-07 
• Released Date: 2009-09-29 
Deposition Author(s): Chumanevich, A.A., Wang, Y.-F., Kovalevsky, A.Y., Weber, I.T.

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations