4CPX

Macrocyclic Transition-State Mimicking HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.308 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Synthesis of P1'-functionalized macrocyclic transition-state mimicking HIV-1 protease inhibitors encompassing a tertiary alcohol.

De Rosa, M.Unge, J.Motwani, H.V.Rosenquist, A.Vrang, L.Wallberg, H.Larhed, M.

(2014) J. Med. Chem. 57: 6444-6457

  • DOI: 10.1021/jm500434q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Seven novel tertiary alcohol containing linear HIV-1 protease inhibitors (PIs), decorated at the para position of the benzyl group in the P1' side with (hetero)aromatic moieties, were synthesized and biologically evaluated. To study the inhibition an ...

    Seven novel tertiary alcohol containing linear HIV-1 protease inhibitors (PIs), decorated at the para position of the benzyl group in the P1' side with (hetero)aromatic moieties, were synthesized and biologically evaluated. To study the inhibition and antiviral activity effect of P1-P3 macrocyclization, 14- and 15-membered macrocyclic PIs were prepared by ring-closing metathesis of the corresponding linear PIs. The macrocycles were more active than the linear precursors and compound 10f, with a 2-thiazolyl group in the P1' position, was the most potent PI of this new series (Ki 2.2 nM, EC50 0.2 μM). Co-crystallized complexes of both linear and macrocyclic PIs with the HIV-1 protease enzyme were prepared and analyzed.


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASE
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 3 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J3W
Query on J3W

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Download CCD File 
A
methyl ~{N}-[(2~{S})-3,3-dimethyl-1-[2-[3-[(3~{R},6~{S},10~{Z})-3-oxidanyl-4,7-bis(oxidanylidene)-6-propan-2-yl-5,8-diazabicyclo[11.2.2]heptadeca-1(16),10,13(17),14-tetraen-3-yl]propyl]-2-[(4-thiophen-2-ylphenyl)methyl]hydrazinyl]-1-oxidanylidene-butan-2-yl]carbamate
C40 H53 N5 O6 S
NERZJFGHXSDKOR-SDGWMEQNSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.308 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.370α = 90.00
b = 86.200β = 90.00
c = 46.220γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
iMOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Data collection
  • Version 2.0: 2019-01-30
    Type: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary