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 
  • R-Value Observed: 0.309 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1021/jm500434q
  • Primary Citation of Related Structures:  
    4COE, 4CP7, 4CPQ, 4CPR, 4CPS, 4CPT, 4CPU, 4CPW, 4CPX

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEASE
A, B
99Human immunodeficiency virusMutation(s): 3 
EC: 3.4.23.16
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J3W
Query on J3W

Download Ideal Coordinates CCD File 
D [auth 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
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B],
F [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.308 
  • R-Value Observed: 0.309 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.37α = 90
b = 86.2β = 90
c = 46.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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