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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.32 kDa 
• Atom Count: 2065 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

4HE9

Crystal Structure of HIV-1 protease mutants I54M complexed with inhibitor GRL-0519

• DOI: 10.2210/pdb4HE9/pdb

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


• Deposited: 2012-10-03 Released: 2013-08-21 
• Deposition Author(s): Shen, C.H., Zhang, H., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.177 
• R-Value Observed: 0.150 

Literature

Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease.

Zhang, H., Wang, Y.F., Shen, C.H., Agniswamy, J., Rao, K.V., Xu, C.X., Ghosh, A.K., Harrison, R.W., Weber, I.T.

(2013) J Med Chem 56: 1074-1083

• PubMed: 23298236 
• DOI: 10.1021/jm301519z
• Primary Citation of Related Structures:  
  4HDB, 4HDF, 4HDP, 4HE9, 4HEG


• PubMed Abstract: 
  

GRL-0519 (1) is a potent antiviral inhibitor of HIV-1 protease (PR) possessing tris-tetrahydrofuran (tris-THF) at P2. The high resolution X-ray crystal structures of inhibitor 1 in complexes with single substitution mutants PR(R8Q), PR(D30N), PR(I50V), PR(I54M), and PR(V82A) were analyzed in relation to kinetic data. The smaller valine side chain in PR(I50V) eliminated hydrophobic interactions with inhibitor and the other subunit consistent with 60-fold worse inhibition. Asn30 in PR(D30N) showed altered interactions with neighboring residues and 18-fold worse inhibition. Mutations V82A and I54M showed compensating structural changes consistent with 6-7-fold lower inhibition. Gln8 in PR(R8Q) replaced the ionic interactions of wild type Arg8 with hydrogen bond interactions without changing the inhibition significantly. The carbonyl oxygen of Gly48 showed two alternative conformations in all structures likely due to the snug fit of the large tris-THF group in the S2 subsite in agreement with high antiviral efficacy of 1 on resistant virus.

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Organizational Affiliation: 

Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 protease	A, B	99	Human immunodeficiency virus type 1 (BRU ISOLATE)	Mutation(s): 6  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G52 (Subject of Investigation/LOI)	C [auth A]	(3R,3aS,3bR,6aS,7aS)-octahydrodifuro[2,3-b:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate C30 H40 N2 O9 S QWMNYFXRFHGYGS-DDGGWZRMSA-N
CL	E [auth A], F [auth A], G [auth B], H [auth B], I [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
G52	Binding MOAD:  4HE9	Ki: 3.5 (nM) from 1 assay(s)
	BindingDB:  4HE9	Ki: min: 0.5, max: 5.9 (nM) from 2 assay(s)
	PDBBind:  4HE9	Ki: 3.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.177 
• R-Value Observed: 0.150 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.776	α = 90
b = 85.842	β = 90
c = 46.017	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	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: 2012-10-03 
• Released Date: 2013-08-21 
Deposition Author(s): Shen, C.H., Zhang, H., Weber, I.T.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release