4M8X | pdb_00004m8x

GS-8374, a Novel Phosphonate-Containing Inhibitor of HIV-1 Protease, Effectively Inhibits HIV PR Mutants with Amino Acid Insertions

• PDB DOI: https://doi.org/10.2210/pdb4M8X/pdb

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


• Deposited: 2013-08-14 Released: 2014-05-07 
• Deposition Author(s): Grantz saskova, K., Brynda, J., Rezacova, P., Kozisek, M., Konvalinka, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

GS-8374, a prototype phosphonate-containing inhibitor of HIV-1 protease, effectively inhibits protease mutants with amino acid insertions.

Grantz Saskova, K., Kozisek, M., Stray, K., de Jong, D., Rezaova, P., Brynda, J., van Maarseveen, N.M., Nijhuis, M., Cihlar, T., Konvalinka, J.

(2014) J Virol 88: 3586-3590

• PubMed: 24371077 
• DOI: https://doi.org/10.1128/JVI.02688-13
• Primary Citation of Related Structures:  
  4M8X, 4M8Y


• PubMed Abstract: 
  

  Insertions in the protease (PR) region of human immunodeficiency virus (HIV) represent an interesting mechanism of antiviral resistance against HIV PR inhibitors (PIs). Here, we demonstrate the improved ability of a phosphonate-containing experimental HIV PI, GS-8374, relative to that of other PIs, to effectively inhibit patient-derived recombinant HIV strains bearing PR insertions and numerous other mutations. We correlate enzyme inhibition with the catalytic activities of corresponding recombinant PRs in vitro and provide a biochemical and structural analysis of the PR-inhibitor complex.

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Organizational Affiliation: 
• Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Prague, Czech Republic.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.02 kDa 
• Atom Count: 1,718 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 8  Gene Names: pol EC: 3.4.23.16
UniProt
Find proteins for Q90JJ9 (Human immunodeficiency virus type 1) Explore Q90JJ9  Go to UniProtKB:  Q90JJ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KGQ	C [auth B], D [auth B]	DIETHYL ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONATE C33 H49 N2 O12 P S FCLYPCIMVVLLRN-FXSYQQGGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.756	α = 90
b = 61.756	β = 90
c = 83.352	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Grantz saskova, K., Brynda, J., Rezacova, P., Kozisek, M., Konvalinka, J.

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description