4A6B

Stereoselective Synthesis, X-ray Analysis, and Biological Evaluation of a New Class of Lactam Based HIV-1 Protease Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Synthesis, X-Ray Analysis, and Biological Evaluation of a New Class of Stereopure Lactam-Based HIV-1 Protease Inhibitors.

Wu, X.Ohrngren, P.Joshi, A.A.Trejos, A.Persson, M.Arvela, R.K.Wallberg, H.Vrang, L.Rosenquist, A.Samuelsson, B.B.Unge, J.Larhed, M.

(2012) J Med Chem 55: 2724

  • DOI: 10.1021/jm201620t
  • Primary Citation of Related Structures:  
    4A4Q, 4A6B, 4A6C

  • PubMed Abstract: 
  • In an effort to identify a new class of druglike HIV-1 protease inhibitors, four different stereopure β-hydroxy γ-lactam-containing inhibitors have been synthesized, biologically evaluated, and cocrystallized. The impact of the tether length of the central spacer (two or three carbons) was also investigated ...

    In an effort to identify a new class of druglike HIV-1 protease inhibitors, four different stereopure β-hydroxy γ-lactam-containing inhibitors have been synthesized, biologically evaluated, and cocrystallized. The impact of the tether length of the central spacer (two or three carbons) was also investigated. A compound with a shorter tether and (3R,4S) absolute configuration exhibited high activity with a K(i) of 2.1 nM and an EC(50) of 0.64 μM. Further optimization by decoration of the P1' side chain furnished an even more potent HIV-1 protease inhibitor (K(i) = 0.8 nM, EC(50) = 0.04 μM). According to X-ray analysis, the new class of inhibitors did not fully succeed in forming two symmetric hydrogen bonds to the catalytic aspartates. The crystal structures of the complexes further explain the difference in potency between the shorter inhibitors (two-carbon spacer) and the longer inhibitors (three-carbon spacer).


    Organizational Affiliation

    Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POL PROTEINA, B99Human immunodeficiency virusMutation(s): 0 
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P35963 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Explore P35963 
Go to UniProtKB:  P35963
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QG8 (Subject of Investigation/LOI)
Query on QG8

Download Ideal Coordinates CCD File 
C [auth B]METHYL ((S)-1-(2-([1,1'-BIPHENYL]-4-YLMETHYL)-2-(3-((3S,4S)-3-BENZYL-4-HYDROXY-1-((1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL)-2-OXOPYRROLIDIN-3-YL)PROPYL)HYDRAZINYL)-3,3-DIMETHYL-1-OXOBUTAN-2-YL)CARBAMATE
C44 H52 N4 O6
YNPGDSJLNVNNFA-MIYQMFTLSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
QG8 Binding MOAD:  4A6B Ki: 12 (nM) from 1 assay(s)
PDBBind:  4A6B Ki: 4.2 (nM) from 1 assay(s)
BindingDB:  4A6B Ki: 12 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.4α = 90
b = 86.5β = 90
c = 46.3γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata 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: 2012-05-09
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Data collection