2BPX

HIV-1 protease-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Rapid X-ray diffraction analysis of HIV-1 protease-inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme.

Munshi, S.Chen, Z.Li, Y.Olsen, D.B.Fraley, M.E.Hungate, R.W.Kuo, L.C.

(1998) Acta Crystallogr D Biol Crystallogr 54: 1053-1060

  • DOI: 10.1107/s0907444998003588
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The ability to replace an inhibitor bound to the HIV-1 protease in single crystals with other potent inhibitors offers the possibility of investigating a series of protease inhibitors rapidly and conveniently with the use of X-ray crystallography. Th ...

    The ability to replace an inhibitor bound to the HIV-1 protease in single crystals with other potent inhibitors offers the possibility of investigating a series of protease inhibitors rapidly and conveniently with the use of X-ray crystallography. This approach affords a fast turnaround of structural information for iterative rational drug designs and obviates the need for studying the complex structures by co-crystallization. The replacement approach has been successfully used with single crystals of the HIV-1 protease complexed with a weak inhibitor. The structures of the complexes obtained by the replacement method are similar to those determined by co-crystallization.


    Related Citations: 
    • Crystal Structure at 1.9-A Resolution of Human Immunodeficiency Virus (HIV) II Protease Complexed with L-735,524, an Orally Bioavailable Inhibitor of the HIV Proteases
      Chen, Z., Li, Y., Chen, E., Hall, D.L., Darke, P.L., Culberson, C., Shafer, J.A., Kuo, L.C.
      (1994) J Biol Chem 269: 26344

    Organizational Affiliation

    Department of Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASEA, B99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: HIV-1 PROTEASE FROM THE NY5 ISOLATE
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 P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5))
Explore P04587 
Go to UniProtKB:  P04587
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MK1
Query on MK1

Download CCD File 
B
N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
C36 H47 N5 O4
CBVCZFGXHXORBI-PXQQMZJSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MK1Ki:  12   nM  BindingDB
MK1-TΔS:  47.2599983215332   kJ/mol  BindingDB
MK1IC50:  61.20000076293945   nM  BindingDB
MK1ΔG:  60.189998626708984   kJ/mol  BindingDB
MK1-TΔS:  60.22999954223633   kJ/mol  BindingDB
MK1-TΔS:  74.02999877929688   kJ/mol  BindingDB
MK1Ki:  15   nM  BindingDB
MK1ΔG:  54.7599983215332   kJ/mol  BindingDB
MK1ΔG:  43.470001220703125   kJ/mol  BindingDB
MK1ΔG:  48.4900016784668   kJ/mol  BindingDB
MK1ΔH:  11.699999809265137   kJ/mol  BindingDB
MK1Ki:  50   nM  BindingDB
MK1-TΔS:  44.75   kJ/mol  BindingDB
MK1Ki:  40   nM  BindingDB
MK1Ki:  0.5199999809265137   nM  BindingDB
MK1-TΔS:  70.2699966430664   kJ/mol  BindingDB
MK1-TΔS:  64.81999969482422   kJ/mol  BindingDB
MK1Ki:  0.2800000011920929   nM  BindingDB
MK1-TΔS:  57.29999923706055   kJ/mol  BindingDB
MK1Ki:  2.640000104904175   nM  BindingDB
MK1ΔH:  31.770000457763672   kJ/mol  BindingDB
MK1ΔH:  15.050000190734863   kJ/mol  BindingDB
MK1ΔG:  38.459999084472656   kJ/mol  BindingDB
MK1ΔH:  12.960000038146973   kJ/mol  BindingDB
MK1-TΔS:  50.599998474121094   kJ/mol  BindingDB
MK1ΔG:  51.83000183105469   kJ/mol  BindingDB
MK1Ki:  0.07000000029802322   nM  BindingDB
MK1ΔH:  13.789999961853027   kJ/mol  BindingDB
MK1Ki:  4.900000095367432   nM  BindingDB
MK1ΔH:  10.869999885559082   kJ/mol  BindingDB
MK1IC50:  0.36000001430511475   nM  BindingDB
MK1ΔH:  15.470000267028809   kJ/mol  BindingDB
MK1ΔH:  9.199999809265137   kJ/mol  BindingDB
MK1-TΔS:  60.63999938964844   kJ/mol  BindingDB
MK1Ki:  3.0999999046325684   nM  BindingDB
MK1ΔH:  27.59000015258789   kJ/mol  BindingDB
MK1ΔH:  14.630000114440918   kJ/mol  BindingDB
MK1Ki:  0.5799999833106995   nM  BindingDB
MK1ΔG:  48.4900016784668   kJ/mol  BindingDB
MK1-TΔS:  42.25   kJ/mol  BindingDB
MK1-TΔS:  65.23999786376953   kJ/mol  BindingDB
MK1-TΔS:  58.13999938964844   kJ/mol  BindingDB
MK1Ki:  69   nM  BindingDB
MK1ΔG:  39.709999084472656   kJ/mol  BindingDB
MK1IC50:  0.6000000238418579   nM  BindingDB
MK1ΔG:  53.5   kJ/mol  BindingDB
MK1ΔG:  53.5   kJ/mol  BindingDB
MK1Ki:  0.5400000214576721   nM  BindingDB
MK1-TΔS:  58.59000015258789   kJ/mol  BindingDB
MK1Ki:  4.400000095367432   nM  BindingDB
MK1IC50:  89   nM  BindingDB
MK1-TΔS:  65.68000030517578   kJ/mol  BindingDB
MK1-TΔS:  58.560001373291016   kJ/mol  BindingDB
MK1Ki:  5.099999904632568   nM  BindingDB
MK1ΔH:  15.470000267028809   kJ/mol  BindingDB
MK1ΔH:  18.389999389648438   kJ/mol  BindingDB
MK1Ki:  2.700000047683716   nM  BindingDB
MK1ΔG:  42.63999938964844   kJ/mol  BindingDB
MK1Ki:  0.10999999940395355   nM  BindingDB
MK1ΔG:  49.31999969482422   kJ/mol  BindingDB
MK1IC50:  0.5899999737739563   nM  BindingDB
MK1ΔH:  12.119999885559082   kJ/mol  BindingDB
MK1IC50:  20.100000381469727   nM  BindingDB
MK1Ki:  0.5400000214576721   nM  BindingDB
MK1IC50:  0.5600000023841858   nM  BindingDB
MK1ΔG:  51   kJ/mol  BindingDB
MK1Ki:  0.800000011920929   nM  BindingDB
MK1Ki:  2.509999990463257   nM  BindingDB
MK1-TΔS:  46.41999816894531   kJ/mol  BindingDB
MK1ΔG:  49.31999969482422   kJ/mol  BindingDB
MK1Ki:  0.550000011920929   nM  BindingDB
MK1IC50:  35   nM  BindingDB
MK1ΔG:  31.770000457763672   kJ/mol  BindingDB
MK1ΔG:  38.459999084472656   kJ/mol  BindingDB
MK1Ki:  108   nM  BindingDB
MK1ΔH:  16.299999237060547   kJ/mol  BindingDB
MK1-TΔS:  55.630001068115234   kJ/mol  BindingDB
MK1ΔG:  51   kJ/mol  BindingDB
MK1Ki:  42   nM  BindingDB
MK1IC50:  61   nM  BindingDB
MK1-TΔS:  62.310001373291016   kJ/mol  BindingDB
MK1Ki:  7.599999904632568   nM  BindingDB
MK1Ki:  1.399999976158142   nM  BindingDB
MK1ΔH:  0   kJ/mol  BindingDB
MK1IC50:  44   nM  BindingDB
MK1ΔG:  57.68000030517578   kJ/mol  BindingDB
MK1IC50:  56   nM  BindingDB
MK1IC50:  0.4099999964237213   nM  BindingDB
MK1IC50:  52   nM  BindingDB
MK1Ki :  0.4000000059604645   nM  PDBBind
MK1-TΔS:  63.150001525878906   kJ/mol  BindingDB
MK1ΔG:  51.40999984741211   kJ/mol  BindingDB
MK1-TΔS:  60.63999938964844   kJ/mol  BindingDB
MK1-TΔS:  64.81999969482422   kJ/mol  BindingDB
MK1IC50:  0.36000001430511475   nM  BindingDB
MK1-TΔS:  49.34000015258789   kJ/mol  BindingDB
MK1Ki:  0.3199999928474426   nM  BindingDB
MK1ΔG:  62.279998779296875   kJ/mol  BindingDB
MK1ΔH:  12.119999885559082   kJ/mol  BindingDB
MK1-TΔS:  59.38999938964844   kJ/mol  BindingDB
MK1Ki:  6.900000095367432   nM  BindingDB
MK1ΔG:  51.83000183105469   kJ/mol  BindingDB
MK1ΔG:  47.650001525878906   kJ/mol  BindingDB
MK1ΔG:  43.470001220703125   kJ/mol  BindingDB
MK1ΔG:  45.13999938964844   kJ/mol  BindingDB
MK1Ki:  27   nM  BindingDB
MK1-TΔS:  65.6500015258789   kJ/mol  BindingDB
MK1Ki:  2.799999952316284   nM  BindingDB
MK1ΔH:  12.539999961853027   kJ/mol  BindingDB
MK1ΔH:  51   kJ/mol  BindingDB
MK1ΔH:  8.779999732971191   kJ/mol  BindingDB
MK1Ki:  0.3700000047683716   nM  BindingDB
MK1-TΔS:  28.030000686645508   kJ/mol  BindingDB
MK1-TΔS:  79.04000091552734   kJ/mol  BindingDB
MK1IC50:  0.5899999737739563   nM  BindingDB
MK1-TΔS:  59.38999938964844   kJ/mol  BindingDB
MK1IC50:  0.8799999952316284   nM  BindingDB
MK1ΔG:  40.54999923706055   kJ/mol  BindingDB
MK1ΔH:  14.630000114440918   kJ/mol  BindingDB
MK1Ki:  398   nM  BindingDB
MK1ΔH:  15.880000114440918   kJ/mol  BindingDB
MK1ΔH:  17.969999313354492   kJ/mol  BindingDB
MK1Ki:  0.3700000047683716   nM  BindingDB
MK1Ki:  1.340000033378601   nM  BindingDB
MK1ΔH:  26.75   kJ/mol  BindingDB
MK1IC50:  370   nM  BindingDB
MK1Ki:  289   nM  BindingDB
MK1Ki:  0.3100000023841858   nM  BindingDB
MK1-TΔS:  65.6500015258789   kJ/mol  BindingDB
MK1ΔH:  27.170000076293945   kJ/mol  BindingDB
MK1-TΔS:  65.23999786376953   kJ/mol  BindingDB
MK1ΔG:  63.119998931884766   kJ/mol  BindingDB
MK1-TΔS:  61.45000076293945   kJ/mol  BindingDB
MK1Ki:  3.0999999046325684   nM  BindingDB
MK1IC50:  0.6000000238418579   nM  BindingDB
MK1ΔG:  62.279998779296875   kJ/mol  BindingDB
MK1-TΔS:  28.860000610351562   kJ/mol  BindingDB
MK1Ki:  3.109999895095825   nM  BindingDB
MK1Ki:  7   nM  BindingDB
MK1ΔH:  24.65999984741211   kJ/mol  BindingDB
MK1ΔH:  14.630000114440918   kJ/mol  BindingDB
MK1Ki:  0.05000000074505806   nM  BindingDB
MK1ΔG:  50.58000183105469   kJ/mol  BindingDB
MK1ΔG:  58.099998474121094   kJ/mol  BindingDB
MK1-TΔS:  71.5   kJ/mol  BindingDB
MK1IC50:  1.600000023841858   nM  BindingDB
MK1ΔG:  53.09000015258789   kJ/mol  BindingDB
MK1Ki:  6.619999885559082   nM  BindingDB
MK1ΔH:  6.690000057220459   kJ/mol  BindingDB
MK1-TΔS:  52.68000030517578   kJ/mol  BindingDB
MK1ΔG:  49.7400016784668   kJ/mol  BindingDB
MK1-TΔS:  82.80000305175781   kJ/mol  BindingDB
MK1ΔG:  38.869998931884766   kJ/mol  BindingDB
MK1ΔG:  44.72999954223633   kJ/mol  BindingDB
MK1Ki:  2.809999942779541   nM  BindingDB
MK1ΔH:  7.940000057220459   kJ/mol  BindingDB
MK1Kd:  1.0700000524520874   nM  BindingDB
MK1ΔH:  2.0899999141693115   kJ/mol  BindingDB
MK1Ki:  0.6000000238418579   nM  BindingDB
MK1-TΔS:  61.900001525878906   kJ/mol  BindingDB
MK1-TΔS:  30.110000610351562   kJ/mol  BindingDB
MK1ΔH:  5.019999980926514   kJ/mol  BindingDB
MK1ΔG:  59.77000045776367   kJ/mol  BindingDB
MK1ΔH:  10.029999732971191   kJ/mol  BindingDB
MK1Ki:  0.23999999463558197   nM  BindingDB
MK1ΔH:  7.519999980926514   kJ/mol  BindingDB
MK1ΔG:  54.34000015258789   kJ/mol  BindingDB
MK1ΔH:  33.439998626708984   kJ/mol  BindingDB
MK1Ki:  10.399999618530273   nM  BindingDB
MK1Ki:  0.36000001430511475   nM  BindingDB
MK1ΔH:  35.11000061035156   kJ/mol  BindingDB
MK1Ki:  2   nM  BindingDB
MK1ΔG:  54.34000015258789   kJ/mol  BindingDB
MK1ΔH:  11.699999809265137   kJ/mol  BindingDB
MK1-TΔS:  58.970001220703125   kJ/mol  BindingDB
MK1ΔH:  10.869999885559082   kJ/mol  BindingDB
MK1ΔG:  47.22999954223633   kJ/mol  BindingDB
MK1ΔH:  8.779999732971191   kJ/mol  BindingDB
MK1ΔH:  9.199999809265137   kJ/mol  BindingDB
MK1ΔH:  20.059999465942383   kJ/mol  BindingDB
MK1-TΔS:  61.900001525878906   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.6α = 90
b = 87.37β = 90
c = 46.64γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1998-01-22 
  • Released Date: 1999-02-23 
  • Deposition Author(s): Munshi, S., Chen, Z.

Revision History 

  • Version 1.0: 1999-02-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-05-09
    Changes: Structure summary