6VCE | pdb_00006vce

HIV-1 wild type protease with GRL-026-18A, a crown-like tetrahydropyranotetrahydrofuran with a bridged methylene group as a P2 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 
    0.155 (Depositor), 0.164 (DCC) 
  • R-Value Work: 
    0.136 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 
    0.137 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Design, Synthesis, and X-ray Studies of Potent HIV-1 Protease Inhibitors with P2-Carboxamide Functionalities.

Ghosh, A.K.Grillo, A.Raghavaiah, J.Kovela, S.Johnson, M.E.Kneller, D.W.Wang, Y.F.Hattori, S.I.Higashi-Kuwata, N.Weber, I.T.Mitsuya, H.

(2020) ACS Med Chem Lett 11: 1965-1972

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00670
  • Primary Citation Related Structures: 
    6VCE

  • PubMed Abstract: 

    The design, synthesis, biological evaluation, and X-ray structural studies are reported for a series of highly potent HIV-1 protease inhibitors. The inhibitors incorporated stereochemically defined amide-based bicyclic and tricyclic ether derivatives as the P2 ligands with ( R )-hydroxyethylaminesulfonamide transition-state isosteres. A number of inhibitors showed excellent HIV-1 protease inhibitory and antiviral activity; however, ligand combination is critical for potency. Inhibitor 4h with a difluorophenylmethyl as the P1 ligand, crown-THF-derived acetamide as the P2 ligand, and a cyclopropylaminobenzothiazole P2'-ligand displayed very potent antiviral activity and maintained excellent antiviral activity against selected multidrug-resistant HIV-1 variants. A high resolution X-ray structure of inhibitor 4h -bound HIV-1 protease provided molecular insight into the binding properties of the new inhibitor.


  • Organizational Affiliation
    • Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.

Macromolecule Content 

  • Total Structure Weight: 22.61 kDa 
  • Atom Count: 2,049 
  • Modeled Residue Count: 198 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03367
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G6R
(Subject of Investigation/LOI)

Query on G6R



Download:Ideal Coordinates CCD File
G [auth B]N-[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]-2-[(3S,3aR,5S,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl]acetamide
C34 H42 F2 N4 O6 S2
BDFWTUGFCVLPRW-KVUOCWAWSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free:  0.155 (Depositor), 0.164 (DCC) 
  • R-Value Work:  0.136 (Depositor), 0.145 (DCC) 
  • R-Value Observed: 0.137 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.904α = 90
b = 86.207β = 90
c = 46.09γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesAI150466
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAI150461
Japan Agency for Medical Research and Development (AMED)JapanJP15fk0410001
Japan Agency for Medical Research and Development (AMED)JapanJP16fk0410101
Other governmentUnited States--
Other governmentJapan--
Other governmentJapan--
Other governmentJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description