6DIL | pdb_00006dil

HIV-1 protease with single mutation L76V in complex with tipranavir

• PDB DOI: https://doi.org/10.2210/pdb6DIL/pdb

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


• Deposited: 2018-05-23 Released: 2018-10-17 
• Deposition Author(s): Wong-Sam, A.E., Wang, Y.-F., Weber, I.T.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.214 (Depositor) 
• R-Value Work: 
  0.163 (Depositor) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease.

Wong-Sam, A., Wang, Y.F., Zhang, Y., Ghosh, A.K., Harrison, R.W., Weber, I.T.

(2018) ACS Omega 3: 12132-12140

• PubMed: 30288468 
• DOI: https://doi.org/10.1021/acsomega.8b01683
• Primary Citation Related Structures: 
  6DIF, 6DIL, 6DJ1, 6DJ2, 6DJ5, 6DJ7


• PubMed Abstract: 
  

  Four HIV-1 protease (PR) inhibitors, clinical inhibitors lopinavir and tipranavir, and two investigational compounds 4 and 5 , were studied for their effect on the structure and activity of PR with drug-resistant mutation L76V (PR _L76V ). Compound 5 exhibited the best K _i value of 1.9 nM for PR _L76V , whereas the other three inhibitors had K _i values of 4.5-7.6 nM, 2-3 orders of magnitude worse than for wild-type enzymes. Crystal structures showed only minor differences in interactions of inhibitors with PR _L76V compared to wild-type complexes. The shorter side chain of Val76 in the mutant lost hydrophobic interactions with Lys45 and Ile47 in the flap, and with Asp30 and Thr74 in the protein core, consistent with decreased stability. Inhibitors forming additional polar interactions with the flaps or dimer interface of PR _L76V were unable to compensate for the decrease in internal hydrophobic contacts. These structures provide insights for inhibitor design.

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Organizational Affiliation: 
• Department of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.
RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.
Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.

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: 22.49 kDa 
• Atom Count: 1,852 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 6  Gene Names: pol
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPV	G [auth B]	N-(3-{(1R)-1-[(6R)-4-HYDROXY-2-OXO-6-PHENETHYL-6-PROPYL-5,6-DIHYDRO-2H-PYRAN-3-YL]PROPYL}PHENYL)-5-(TRIFLUOROMETHYL)-2-PYRIDINESULFONAMIDE C31 H33 F3 N2 O5 S SUJUHGSWHZTSEU-FYBSXPHGSA-N
GOL	E [auth A], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	D [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.214 (Depositor) 
• R-Value Work:  0.163 (Depositor) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.604	α = 90
b = 86.403	β = 90
c = 46.156	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Wong-Sam, A.E., Wang, Y.-F., Weber, I.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM062920

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description