1HXW

HIV-1 PROTEASE DIMER COMPLEXED WITH A-84538


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

ABT-538 is a potent inhibitor of human immunodeficiency virus protease and has high oral bioavailability in humans.

Kempf, D.J.Marsh, K.C.Denissen, J.F.McDonald, E.Vasavanonda, S.Flentge, C.A.Green, B.E.Fino, L.Park, C.H.Kong, X.P.

(1995) Proc Natl Acad Sci U S A 92: 2484-2488

  • DOI: 10.1073/pnas.92.7.2484
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Examination of the structural basis for antiviral activity, oral pharmacokinetics, and hepatic metabolism among a series of symmetry-based inhibitors of the human immunodeficiency virus (HIV) protease led to the discovery of ABT-538, a promising expe ...

    Examination of the structural basis for antiviral activity, oral pharmacokinetics, and hepatic metabolism among a series of symmetry-based inhibitors of the human immunodeficiency virus (HIV) protease led to the discovery of ABT-538, a promising experimental drug for the therapeutic intervention in acquired immunodeficiency syndrome (AIDS). ABT-538 exhibited potent in vitro activity against laboratory and clinical strains of HIV-1 [50% effective concentration (EC50) = 0.022-0.13 microM] and HIV-2 (EC50 = 0.16 microM). Following a single 10-mg/kg oral dose, plasma concentrations in rat, dog, and monkey exceeded the in vitro antiviral EC50 for > 12 h. In human trials, a single 400-mg dose of ABT-538 displayed a prolonged absorption profile and achieved a peak plasma concentration in excess of 5 micrograms/ml. These findings demonstrate that high oral bioavailability can be achieved in humans with peptidomimetic inhibitors of HIV protease.


    Organizational Affiliation

    Department of Anti-Infective Research, Abbott Laboratories, Abbott Laboratories, Abbott Park, IL 60064, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
Go to UniProtKB:  P12499
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RIT
Query on RIT

Download CCD File 
B
RITONAVIR
C37 H48 N6 O5 S2
NCDNCNXCDXHOMX-XGKFQTDJSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001001 (RIT)
Query on PRD_001001
BRITONAVIRPeptide-like /  Inhibitor

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RITΔG:  35.529998779296875   kJ/mol  BindingDB
RITKd:  0.6000000238418579   nM  BindingDB
RITΔG:  36.369998931884766   kJ/mol  BindingDB
RITΔH:  3.759999990463257   kJ/mol  BindingDB
RITΔH:  15.050000190734863   kJ/mol  BindingDB
RIT-TΔS:  80.29000091552734   kJ/mol  BindingDB
RIT-TΔS:  79.04000091552734   kJ/mol  BindingDB
RITΔG:  57.68000030517578   kJ/mol  BindingDB
RITKi:  0.11999999731779099   nM  BindingDB
RITKi:  0.699999988079071   nM  BindingDB
RIT-TΔS:  42.63999938964844   kJ/mol  BindingDB
RITΔH:  40.130001068115234   kJ/mol  BindingDB
RIT-TΔS:  52.68000030517578   kJ/mol  BindingDB
RITKi:  2.4000000953674316   nM  BindingDB
RITKd:  0.6100000143051147   nM  BindingDB
RITΔH:  12.119999885559082   kJ/mol  BindingDB
RITΔH:  10.869999885559082   kJ/mol  BindingDB
RIT-TΔS:  56.86000061035156   kJ/mol  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RITKi:  0.05999999865889549   nM  BindingDB
RITΔG:  44.72999954223633   kJ/mol  BindingDB
RITΔH:  12.960000038146973   kJ/mol  BindingDB
RITΔG:  45.97999954223633   kJ/mol  BindingDB
RITΔH:  51   kJ/mol  BindingDB
RITKi:  0.15000000596046448   nM  BindingDB
RITKi:  60   nM  BindingDB
RITΔG:  49.31999969482422   kJ/mol  BindingDB
RITΔH:  15.470000267028809   kJ/mol  BindingDB
RITΔH:  35.95000076293945   kJ/mol  BindingDB
RIT-TΔS:  69.83000183105469   kJ/mol  BindingDB
RITKi:  1.2000000476837158   nM  BindingDB
RIT-TΔS:  34.70000076293945   kJ/mol  BindingDB
RITΔH:  26.75   kJ/mol  BindingDB
RITΔH:  2.0899999141693115   kJ/mol  BindingDB
RIT-TΔS:  30.110000610351562   kJ/mol  BindingDB
RITΔG:  50.15999984741211   kJ/mol  BindingDB
RIT-TΔS:  33.040000915527344   kJ/mol  BindingDB
RIT-TΔS:  65.6500015258789   kJ/mol  BindingDB
RITΔH:  15.470000267028809   kJ/mol  BindingDB
RITKi:  0.019999999552965164   nM  BindingDB
RITKi:  0.015000000596046448   nM  Binding MOAD
RITΔG:  33.439998626708984   kJ/mol  BindingDB
RIT-TΔS:  46.41999816894531   kJ/mol  BindingDB
RIT-TΔS:  43.91999816894531   kJ/mol  BindingDB
RITΔG:  54.7599983215332   kJ/mol  BindingDB
RITIC50:  67   nM  BindingDB
RIT-TΔS:  60.63999938964844   kJ/mol  BindingDB
RITΔG:  60.189998626708984   kJ/mol  BindingDB
RITΔG:  43.470001220703125   kJ/mol  BindingDB
RITΔG:  56.0099983215332   kJ/mol  BindingDB
RITΔG:  56.43000030517578   kJ/mol  BindingDB
RITΔG:  51.83000183105469   kJ/mol  BindingDB
RITΔG:  38.040000915527344   kJ/mol  BindingDB
RITΔG:  52.25   kJ/mol  BindingDB
RIT-TΔS:  43.91999816894531   kJ/mol  BindingDB
RITΔG:  55.18000030517578   kJ/mol  BindingDB
RITΔH:  40.130001068115234   kJ/mol  BindingDB
RITKi:  32   nM  BindingDB
RITKi:  0.9100000262260437   nM  BindingDB
RITKi:  1.100000023841858   nM  BindingDB
RIT-TΔS:  76.94999694824219   kJ/mol  BindingDB
RITΔG:  31.770000457763672   kJ/mol  BindingDB
RITKi:  109   nM  BindingDB
RITKi:  0.019999999552965164   nM  BindingDB
RIT-TΔS:  58.560001373291016   kJ/mol  BindingDB
RITΔH:  22.56999969482422   kJ/mol  BindingDB
RITKi:  0.23000000417232513   nM  BindingDB
RITKi:  0.46000000834465027   nM  BindingDB
RITΔH:  73.1500015258789   kJ/mol  BindingDB
RITΔH:  0   kJ/mol  BindingDB
RITΔG:  28.84000015258789   kJ/mol  BindingDB
RIT-TΔS:  58.59000015258789   kJ/mol  BindingDB
RIT-TΔS:  30.110000610351562   kJ/mol  BindingDB
RITKi :  0.015000000596046448   nM  PDBBind
RITΔG:  38.869998931884766   kJ/mol  BindingDB
RITΔH:  4.599999904632568   kJ/mol  BindingDB
RIT-TΔS:  57.33000183105469   kJ/mol  BindingDB
RIT-TΔS:  46.84000015258789   kJ/mol  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RITΔH:  5.019999980926514   kJ/mol  BindingDB
RITΔH:  9.199999809265137   kJ/mol  BindingDB
RITΔH:  24.239999771118164   kJ/mol  BindingDB
RITΔH:  30.510000228881836   kJ/mol  BindingDB
RITΔH:  12.960000038146973   kJ/mol  BindingDB
RITKi:  0.029999999329447746   nM  BindingDB
RITΔH:  9.609999656677246   kJ/mol  BindingDB
RIT-TΔS:  43.08000183105469   kJ/mol  BindingDB
RITΔG:  45.13999938964844   kJ/mol  BindingDB
RIT-TΔS:  75.27999877929688   kJ/mol  BindingDB
RIT-TΔS:  44.75   kJ/mol  BindingDB
RITΔH:  13.789999961853027   kJ/mol  BindingDB
RITKi:  0.20000000298023224   nM  BindingDB
RITΔH:  12.539999961853027   kJ/mol  BindingDB
RITKi:  30   nM  BindingDB
RITΔH:  43.470001220703125   kJ/mol  BindingDB
RIT-TΔS:  76.54000091552734   kJ/mol  BindingDB
RITΔH:  27.59000015258789   kJ/mol  BindingDB
RITΔG:  41.79999923706055   kJ/mol  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RITΔG:  49.31999969482422   kJ/mol  BindingDB
RIT-TΔS:  42.25   kJ/mol  BindingDB
RITΔG:  42.63999938964844   kJ/mol  BindingDB
RIT-TΔS:  45.59000015258789   kJ/mol  BindingDB
RITKi:  0.5   nM  BindingDB
RITΔG:  40.959999084472656   kJ/mol  BindingDB
RITΔG:  39.709999084472656   kJ/mol  BindingDB
RITKi:  0.3700000047683716   nM  BindingDB
RIT-TΔS:  102.05999755859375   kJ/mol  BindingDB
RITΔH:  12.119999885559082   kJ/mol  BindingDB
RIT-TΔS:  64.81999969482422   kJ/mol  BindingDB
RITKi:  15   nM  BindingDB
RIT-TΔS:  65.23999786376953   kJ/mol  BindingDB
RITKi:  23   nM  BindingDB
RITΔH:  21.739999771118164   kJ/mol  BindingDB
RITΔH:  8.779999732971191   kJ/mol  BindingDB
RITΔG:  36.779998779296875   kJ/mol  BindingDB
RITΔG:  34.279998779296875   kJ/mol  BindingDB
RIT-TΔS:  50.27000045776367   kJ/mol  BindingDB
RITΔH:  25.079999923706055   kJ/mol  BindingDB
RITΔG:  52.66999816894531   kJ/mol  BindingDB
RITΔG:  53.91999816894531   kJ/mol  BindingDB
RITΔG:  57.27000045776367   kJ/mol  BindingDB
RIT-TΔS:  36.369998931884766   kJ/mol  BindingDB
RITΔG:  45.560001373291016   kJ/mol  BindingDB
RITΔG:  44.310001373291016   kJ/mol  BindingDB
RITΔG:  54.34000015258789   kJ/mol  BindingDB
RITKi:  0.699999988079071   nM  BindingDB
RITKi:  40   nM  BindingDB
RITΔG:  55.59000015258789   kJ/mol  BindingDB
RITΔH:  14.630000114440918   kJ/mol  BindingDB
RITKi:  3.0999999046325684   nM  BindingDB
RITΔG:  40.130001068115234   kJ/mol  BindingDB
RIT-TΔS:  51.0099983215332   kJ/mol  BindingDB
RITKi:  4   nM  BindingDB
RITKi:  13   nM  BindingDB
RITΔH:  0.07999999821186066   kJ/mol  BindingDB
RITΔH:  12.960000038146973   kJ/mol  BindingDB
RIT-TΔS:  57.29999923706055   kJ/mol  BindingDB
RITΔG:  49.7400016784668   kJ/mol  BindingDB
RITΔH:  17.969999313354492   kJ/mol  BindingDB
RITΔH:  11.699999809265137   kJ/mol  BindingDB
RIT-TΔS:  70.2699966430664   kJ/mol  BindingDB
RITΔG:  40.54999923706055   kJ/mol  BindingDB
RIT-TΔS:  62.7599983215332   kJ/mol  BindingDB
RITKi:  3.0199999809265137   nM  BindingDB
RITΔH:  17.559999465942383   kJ/mol  BindingDB
RITKi:  0.3700000047683716   nM  BindingDB
RITΔH:  2.930000066757202   kJ/mol  BindingDB
RIT-TΔS:  66.48999786376953   kJ/mol  BindingDB
RIT-TΔS:  82.80000305175781   kJ/mol  BindingDB
RITΔG:  45.560001373291016   kJ/mol  BindingDB
RITΔH:  11.699999809265137   kJ/mol  BindingDB
RIT-TΔS:  70.2699966430664   kJ/mol  BindingDB
RIT-TΔS:  39.29999923706055   kJ/mol  BindingDB
RITKi:  4.5   nM  BindingDB
RITKi:  0.05999999865889549   nM  BindingDB
RIT-TΔS:  43.08000183105469   kJ/mol  BindingDB
RITKi:  0.5899999737739563   nM  BindingDB
RITΔH:  33.439998626708984   kJ/mol  BindingDB
RIT-TΔS:  35.540000915527344   kJ/mol  BindingDB
RITΔH:  12.119999885559082   kJ/mol  BindingDB
RITΔH:  43.470001220703125   kJ/mol  BindingDB
RITKi:  2.809999942779541   nM  BindingDB
RITΔH:  8.359999656677246   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.06α = 90
b = 86.88β = 90
c = 46.62γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
R-AXISdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-02-04
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other