3ZPU

Design and Synthesis of P1-P3 Macrocyclic Tertiary Alcohol Comprising HIV-1 Protease Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design and Synthesis of P1-P3 Macrocyclic Tertiary Alcohol Comprising HIV-1 Protease Inhibitors

Joshi, A.Veron, J.B.Unge, J.Rosenquist, A.Wallberg, H.Samuelsson, B.Hallberg, A.Larhed, M.

(2013) J.Med.Chem. 56: 8999

  • DOI: 10.1021/jm400811d
  • Primary Citation of Related Structures:  3ZPS, 3ZPT

  • PubMed Abstract: 
  • To study P1-P3 macrocyclizations of previously reported tertiary-alcohol-comprising HIV-1 protease inhibitors (PIs), three new 14- and 15-member macrocyclic PIs were designed, synthesized by ring-closing metathesis, and evaluated alongside with 10 no ...

    To study P1-P3 macrocyclizations of previously reported tertiary-alcohol-comprising HIV-1 protease inhibitors (PIs), three new 14- and 15-member macrocyclic PIs were designed, synthesized by ring-closing metathesis, and evaluated alongside with 10 novel linear PIs. Cocrystallized complexes of the macrocyclic PIs and the HIV-1 protease are presented, analyzed, and discussed. The macrocyclic structures exhibited higher activities than the linear precursors with Ki and EC50 values down to 3.1 nM and 0.37 μM, respectively.


    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 BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
M8B
Query on M8B

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Download CCD File 
B
methyl N-[(2S)-1-[2-[(4-bromophenyl)methyl]-2-[3-[(3Z,8S,11R)-8-tert-butyl-11-oxidanyl-7,10-bis(oxidanylidene)-6,9-diazabicyclo[11.2.2]heptadeca-1(15),3,13,16-tetraen-11-yl]propyl]hydrazinyl]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate
C37 H52 Br N5 O6
SFNMYSUIYNOTIA-HIOXXDBGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M8BKi: 4.2 nM BINDINGMOAD
M8BKi: 4.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.330α = 90.00
b = 86.120β = 90.00
c = 46.290γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection