Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22322.40 
• Atom Count: 1822 
• 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 group M subtype B
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 6 


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

---

Experimental Data Snapshot

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

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:  
  4HEG, 4HDP, 4HDF, 4HDB


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 protease	A, B	99	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 6  Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P03367

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
G52	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
G52	Ki: 3.5 nM BINDINGMOAD
G52	Ki: 3.5 nM PDBBIND

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 58.776	α = 90.00
b = 85.842	β = 90.00
c = 46.017	γ = 90.00

Software Package:

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

Structure Validation

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