5TUQ

Crystal Structure of a 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione Inhibitor in Complex with HIV Reverse Transcriptase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.705 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione as an inhibitor scaffold of HIV reverase transcriptase: Impacts of the 3-OH on inhibiting RNase H and polymerase.

Tang, J.Kirby, K.A.Huber, A.D.Casey, M.C.Ji, J.Wilson, D.J.Sarafianos, S.G.Wang, Z.

(2017) Eur J Med Chem 128: 168-179

  • DOI: 10.1016/j.ejmech.2017.01.041

  • PubMed Abstract: 
  • 3-Hydroxypyrimidine-2,4-dione (HPD) represents a versatile chemical core in the design of inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H and integrase strand transfer (INST). We report herein the design ...

    3-Hydroxypyrimidine-2,4-dione (HPD) represents a versatile chemical core in the design of inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H and integrase strand transfer (INST). We report herein the design, synthesis and biological evaluation of an HPD subtype (4) featuring a cyclohexylmethyl group at the C-6 position. Antiviral testing showed that most analogues of 4 inhibited HIV-1 in the low nanomolar to submicromolar range, without cytotoxicity at concentrations up to 100 μM. Biochemically, these analogues dually inhibited both the polymerase (pol) and the RNase H functions of RT, but not INST. Co-crystal structure of 4a with RT revealed a nonnucleoside RT inhibitor (NNRTI) binding mode. Interestingly, chemotype 11, the synthetic precursor of 4 lacking the 3-OH group, did not inhibit RNase H while potently inhibiting pol. By virtue of the potent antiviral activity and biochemical RNase H inhibition, HPD subtype 4 could provide a viable platform for eventually achieving potent and selective RNase H inhibition through further medicinal chemistry.


    Organizational Affiliation

    Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE
A
557Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE
B
429Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 1 
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
J63
Query on J63

Download SDF File 
Download CCD File 
A
1-[(benzyloxy)methyl]-6-(cyclohexylmethyl)-3-hydroxy-5-(propan-2-yl)pyrimidine-2,4(1H,3H)-dione
C22 H30 N2 O4
ROZLWEMOPMWULZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.705 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 161.901α = 90.00
b = 72.355β = 99.87
c = 107.334γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI100890

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence