2HB3 | pdb_00002hb3

Wild-type HIV-1 Protease in complex with potent inhibitor GRL06579


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.192 (Depositor) 
  • R-Value Work: 
    0.147 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2HB3

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure-Based Design of Novel HIV-1 Protease Inhibitors To Combat Drug Resistance.

Ghosh, A.K.Sridhar, P.R.Leshchenko, S.Hussain, A.K.Li, J.Kovalevsky, A.Y.Walters, D.E.Wedekind, J.E.Grum-Tokars, V.Das, D.Koh, Y.Maeda, K.Gatanaga, H.Weber, I.T.Mitsuya, H.

(2006) J Med Chem 49: 5252-5261

  • DOI: https://doi.org/10.1021/jm060561m
  • Primary Citation Related Structures: 
    2HB3

  • PubMed Abstract: 

    Structure-based design and synthesis of novel HIV protease inhibitors are described. The inhibitors are designed specifically to interact with the backbone of HIV protease active site to combat drug resistance. Inhibitor 3 has exhibited exceedingly potent enzyme inhibitory and antiviral potency. Furthermore, this inhibitor maintains impressive potency against a wide spectrum of HIV including a variety of multi-PI-resistant clinical strains. The inhibitors incorporated a stereochemically defined 5-hexahydrocyclopenta[b]furanyl urethane as the P2-ligand into the (R)-(hydroxyethylamino)sulfonamide isostere. Optically active (3aS,5R,6aR)-5-hydroxy-hexahydrocyclopenta[b]furan was prepared by an enzymatic asymmetrization of meso-diacetate with acetyl cholinesterase, radical cyclization, and Lewis acid-catalyzed anomeric reduction as the key steps. A protein-ligand X-ray crystal structure of inhibitor 3-bound HIV-1 protease (1.35 A resolution) revealed extensive interactions in the HIV protease active site including strong hydrogen bonding interactions with the backbone. This design strategy may lead to novel inhibitors that can combat drug resistance.


  • Organizational Affiliation
    • Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, USA. akghosh@purdue.edu

Macromolecule Content 

  • Total Structure Weight: 22.29 kDa 
  • Atom Count: 1,837 
  • 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: GAGPOL
EC: 3.4.23.4
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GRL

Query on GRL



Download:Ideal Coordinates CCD File
H [auth B](3AS,5R,6AR)-HEXAHYDRO-2H-CYCLOPENTA[B]FURAN-5-YL (2S,3S)-3-HYDROXY-4-(4-(HYDROXYMETHYL)-N-ISOBUTYLPHENYLSULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE
C29 H40 N2 O7 S
VYBDPVQMILRSMK-GRXYLYAXSA-N
GOL

Query on GOL



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

Query on CL



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

Query on NA



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.192 (Depositor) 
  • R-Value Work:  0.147 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.08α = 90
b = 86.48β = 90
c = 45.94γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection