2Q55 | pdb_00002q55

Crystal structure of KK44 bound to HIV-1 protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.235 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.178 (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 1.5 of the entry. See complete history

Literature

Design and Synthesis of HIV-1 Protease Inhibitors Incorporating Oxazolidinones as P2/P2' Ligands in Pseudosymmetric Dipeptide Isosteres.

Reddy, G.S.Ali, A.Nalam, M.N.Anjum, S.G.Cao, H.Nathans, R.S.Schiffer, C.A.Rana, T.M.

(2007) J Med Chem 50: 4316-4328

  • DOI: https://doi.org/10.1021/jm070284z
  • Primary Citation Related Structures: 
    2Q54, 2Q55, 2Q5K

  • PubMed Abstract: 

    A series of novel HIV-1 protease inhibitors based on two pseudosymmetric dipeptide isosteres have been synthesized and evaluated. The inhibitors were designed by incorporating N-phenyloxazolidinone-5-carboxamides into the hydroxyethylene and (hydroxyethyl)hydrazine dipeptide isosteres as P2 and P2' ligands. Compounds with (S)-phenyloxazolidinones attached at a position proximal to the central hydroxyl group showed low nM inhibitory activities against wild-type HIV-1 protease. Selected compounds were further evaluated for their inhibitory activities against a panel of multidrug-resistant protease variants and for their antiviral potencies in MT-4 cells. The crystal structures of lopinavir (LPV) and two new inhibitors containing phenyloxazolidinone-based ligands in complex with wild-type HIV-1 protease have been determined. A comparison of the inhibitor-protease structures with the LPV-protease structure provides valuable insight into the binding mode of the new inhibitors to the protease enzyme. Based on the crystal structures and knowledge of structure-activity relationships, new inhibitors can be designed with enhanced enzyme inhibitory and antiviral potencies.


  • Organizational Affiliation
    • Chemical Biology Program and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

Macromolecule Content 

  • Total Structure Weight: 22.48 kDa 
  • Atom Count: 1,700 
  • 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): 1 
Gene Names: pol
UniProt
Find proteins for O38719 (Human immunodeficiency virus type 1)
Explore O38719 
Go to UniProtKB:  O38719
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO38719
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MU0

Query on MU0



Download:Ideal Coordinates CCD File
E [auth B](5S)-N-[(1S,2S,4S)-1-BENZYL-2-HYDROXY-4-{[(2S)-3-METHYL-2-(2-OXOTETRAHYDROPYRIMIDIN-1(2H)-YL)BUTANOYL]AMINO}-5-PHENYLPENTYL]-2-OXO-3-PHENYL-1,3-OXAZOLIDINE-5-CARBOXAMIDE
C37 H45 N5 O6
YTEURAFEAFHROU-FLIXOAOSSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.235 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.844α = 90
b = 58.53β = 90
c = 61.869γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy, Structure summary