Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 22.18 kDa 
• Atom Count: 1724 
• Residue Count: 198 
• Unique protein chains: 1

4I8Z

Crystal structure of wild type HIV-1 protease in complex with non-peptidic inhibitor, GRL008

• DOI: 10.2210/pdb4I8Z/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-12-04 Released: 2013-07-24 
• Deposition Author(s): Yedidi, R.S., Palmer, I., Das, D., Wingfield, P.T., Ghosh, A.K., Mitsuya, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.220 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

P2' benzene carboxylic acid moiety is associated with decrease in cellular uptake: evaluation of novel non-peptidic HIV-1 protease inhibitors containing P2 bis-tetrahydrofuran moiety.

Yedidi, R.S., Maeda, K., Fyvie, W.S., Steffey, M., Davis, D.A., Palmer, I., Aoki, M., Kaufman, J.D., Stahl, S.J., Garimella, H., Das, D., Wingfield, P.T., Ghosh, A.K., Mitsuya, H.

(2013) Antimicrob Agents Chemother 57: 4920-4927

• PubMed: 23877703 
• DOI: 10.1128/AAC.00868-13
• Structures With Same Primary Citation


• PubMed Abstract: 
  

GRL007 and GRL008, two structurally related nonpeptidic human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) containing 3(R),3a(S),6a(R)-bis-tetrahydrofuranylurethane (bis-THF) as the P2 moiety and a sulfonamide isostere consisting of benzene carboxylic acid and benzene carboxamide as the P2' moiety, respectively, were evaluated for their antiviral activity and interactions with wild-type protease (PR(WT)). Both GRL007 (Ki of 12.7 pM with PR(WT)) and GRL008 (Ki of 8.9 pM) inhibited PR(WT) with high potency in vitro. X-ray crystallographic analysis of PR(WT) in complex with GRL007 or GRL008 showed that the bis-THF moiety of both compounds has three direct polar contacts with the backbone amide nitrogen atoms of Asp29 and Asp30 of PR(WT). The P2' moiety of both compounds showed one direct contact with the backbone of Asp30' and a bridging polar contact with Gly48' through a water molecule. Cell-based antiviral assays showed that GRL007 was inactive (50% effective concentration [EC50] of >1 μM) while GRL008 was highly active (EC50 of 0.04 μM) against wild-type HIV-1. High-performance liquid chromatography (HPLC)/mass spectrometry-based cellular uptake assays showed 8.1- and 84-fold higher intracellular concentrations of GRL008 than GRL007 in human MT-2 and MT-4 cell extracts, respectively. Thus, GRL007, in spite of its favorable enzyme-inhibitory activity and protease binding profile, exhibited a lack of antiviral activity in cell-based assays, most likely due to its compromised cellular uptake associated with its P2' benzene carboxylic acid moiety. The anti-HIV-1 potency, favorable toxicity, and binding profile of GRL008 suggest that further optimization of the P2' moiety may improve its antiretroviral features.

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Organizational Affiliation: 

Experimental Retrovirology Section.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  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 P0C6F2 (Human immunodeficiency virus type 1 group M subtype B (isolate LW123)) Go to UniProtKB:  P0C6F2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G08	A	(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[(4-carbamoylphenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate C28 H37 N3 O8 S VYMACSGLMLFUSD-GAYSTUHSSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
G08	Ki:  0.008899999782443047   nM  PDBBind
G08	Ki:  0.008899999782443047   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.220 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.12	α = 90
b = 62.12	β = 90
c = 81.74	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-04 
• Released Date: 2013-07-24 
Deposition Author(s): Yedidi, R.S., Palmer, I., Das, D., Wingfield, P.T., Ghosh, A.K., Mitsuya, H.

Revision History 

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2013-09-25
  Changes: Database references