1EET

HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH THE INHIBITOR MSC204

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

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This is version 1.3 of the entry. See complete history. 


Literature

Urea-PETT compounds as a new class of HIV-1 reverse transcriptase inhibitors. 3. Synthesis and further structure-activity relationship studies of PETT analogues.

Hogberg, M., Sahlberg, C., Engelhardt, P., Noreen, R., Kangasmetsa, J., Johansson, N.G., Oberg, B., Vrang, L., Zhang, H., Sahlberg, B.L., Unge, T., Lovgren, S., Fridborg, K., Backbro, K.

(1999) J Med Chem 42: 4150-4160

  • DOI: 10.1021/jm990095j
  • Primary Citation of Related Structures:  
    1EET

  • PubMed Abstract: 

    • The further development of allosteric HIV-1 RT inhibitors in the urea analogue series of PETT (phenylethylthiazolylthiourea) derivatives is described here. The series includes derivatives with an ethyl linker (1-5) and racemic (6-16) and enantiomeric (17-20) cis-cyclopropane compounds ...

    The further development of allosteric HIV-1 RT inhibitors in the urea analogue series of PETT (phenylethylthiazolylthiourea) derivatives is described here. The series includes derivatives with an ethyl linker (1-5) and racemic (6-16) and enantiomeric (17-20) cis-cyclopropane compounds. The antiviral activity was determined both at the RT level and in cell culture on both wild-type and mutant forms of HIV-1. Most compounds have anti-HIV-1 activity on the wt in the nanomolar range. Resistant HIV-1 was selected in vitro for some of the compounds, and the time for resistant HIV-1 to develop was longer for urea-PETT compounds than it was for reference compounds. Preliminary pharmacokinetics in rats showed that compound 18 is orally bioavailable and penetrates well into the brain. The three-dimensional structure of complexes between HIV-1 RT and two enantiomeric compounds (17 and 18) have been determined. The structures show similar binding in the NNI binding pocket. The propionylphenyl moieties of both inhibitors show perfect stacking to tyrosine residues 181 and 188. The cyclopropyl moiety of the (+)-enantiomer 18 exhibits optimal packing distances for the interactions with leucine residue 100 and valine residue 179.

    Organizational Affiliation: 

    Medivir AB, Lunastigen 7, S-141 44 Huddinge, Sweden.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASEA557Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: BH10
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (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 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
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASEB427Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: BH10
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (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 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BFU
Query on BFU
Download Ideal Coordinates CCD File 
C [auth A]1-(5-BROMO-PYRIDIN-2-YL)-3-[2-(6-FLUORO-2-HYDROXY-3-PROPIONYL-PHENYL)-CYCLOPROPYL]-UREA
C18 H17 Br F N3 O3
VRAJWAGCJIXJHQ-YPMHNXCESA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BFU BindingDB:  1EET IC50: min: 4.8, max: 41 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.57α = 90
b = 156.45β = 90
c = 156.35γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations