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: 22.55 kDa 
• Atom Count: 1970 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

4KB9

Crystal structure of wild-type HIV-1 protease with novel tricyclic P2-ligands GRL-0739A

• DOI: 10.2210/pdb4KB9/pdb

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


• Deposited: 2013-04-23 Released: 2013-09-04 
• Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.180 
• R-Value Work: 0.139 
• R-Value Observed: 0.139 

Literature

Highly Potent HIV-1 Protease Inhibitors with Novel Tricyclic P2 Ligands: Design, Synthesis, and Protein-Ligand X-ray Studies.

Ghosh, A.K., Parham, G.L., Martyr, C.D., Nyalapatla, P.R., Osswald, H.L., Agniswamy, J., Wang, Y.F., Amano, M., Weber, I.T., Mitsuya, H.

(2013) J Med Chem 56: 6792-6802

• PubMed: 23947685 
• DOI: 10.1021/jm400768f
• Primary Citation of Related Structures:  
  4KB9


• PubMed Abstract: 
  

The design, synthesis, and biological evaluation of a series of HIV-1 protease inhibitors incorporating stereochemically defined fused tricyclic P2 ligands are described. Various substituent effects were investigated to maximize the ligand-binding site interactions in the protease active site. Inhibitors 16a and 16f showed excellent enzyme inhibitory and antiviral activity, although the incorporation of sulfone functionality resulted in a decrease in potency. Both inhibitors 16a and 16f maintained activity against a panel of multidrug resistant HIV-1 variants. A high-resolution X-ray crystal structure of 16a-bound HIV-1 protease revealed important molecular insights into the ligand-binding site interactions, which may account for the inhibitor's potent antiviral activity and excellent resistance profiles.

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Organizational Affiliation: 

Department of Chemistry and Department of Medicinal Chemistry, Purdue University , West Lafayette, Indiana 47907, 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
Find proteins for Q7SSI0 (Human immunodeficiency virus 1) Explore Q7SSI0  Go to UniProtKB:  Q7SSI0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G79 (Subject of Investigation/LOI)	C [auth A]	(3aR,3bR,4S,7aR,8aS)-decahydrofuro[2,3-b][1]benzofuran-4-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate C32 H44 N2 O8 S ORJPZJYXIFRPSW-OTTDUJIMSA-N
GOL	J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], F [auth A], I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	D [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
G79	Binding MOAD:  4KB9	Ki: 1.00e-2 (nM) from 1 assay(s)
	PDBBind:  4KB9	Ki: 1.00e-2 (nM) from 1 assay(s)
	BindingDB:  4KB9	Ki: 1.00e-2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.180 
• R-Value Work: 0.139 
• R-Value Observed: 0.139 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.477	α = 90
b = 86.3	β = 90
c = 46.045	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2013-04-23 
• Released Date: 2013-09-04 
Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2013-09-25
  Changes: Database references