2R5P

Crystal Structure Analysis of HIV-1 Subtype C Protease Complexed with Indinavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Contribution of Naturally Occurring Polymorphisms in Altering the Biochemical and Structural Characteristics of HIV-1 Subtype C Protease

Coman, R.M.Robbins, A.H.Fernandez, M.A.Gilliland, C.T.Sochet, A.A.Goodenow, M.M.McKenna, R.Dunn, B.M.

(2008) Biochemistry 47: 731-743

  • DOI: 10.1021/bi7018332
  • Primary Citation of Related Structures:  
    2R5Q, 2R5P

  • PubMed Abstract: 
  • Fourteen subtype B and C protease variants have been engineered in an effort to study whether the preexistent baseline polymorphisms, by themselves or in combination with drug resistance mutations, differentially alter the biochemical and structural ...

    Fourteen subtype B and C protease variants have been engineered in an effort to study whether the preexistent baseline polymorphisms, by themselves or in combination with drug resistance mutations, differentially alter the biochemical and structural features of the subtype C protease when compared with those of subtype B protease. The kinetic studies performed in this work showed that the preexistent polymorphisms in subtype C protease, by themselves, do not provide for a greater level of resistance. Inhibition analysis with eight clinically used protease inhibitors revealed that the natural polymorphisms found in subtype C protease, in combination with drug resistance mutations, can influence enzymatic catalytic efficiency and inhibitor resistance. Structural analyses of the subtype C protease bound to nelfinavir and indinavir showed that these inhibitors form similar interactions with the residues in the active site of subtype B and C proteases. It also revealed that the naturally occurring polymorphisms could alter the position of the outer loops of the subtype C protease, especially the 60's loop.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610, USA



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseABCD99Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: pol
EC: 3.4.23.16 (UniProt), 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 O12158 (Human immunodeficiency virus type 1 group M subtype C (isolate 92BR025))
Explore O12158 
Go to UniProtKB:  O12158
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MK1
Query on MK1

Download CCD File 
B, D
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
CL
Query on CL

Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MK1-TΔS:  50.599998474121094   kJ/mol  BindingDB
MK1ΔH:  7.940000057220459   kJ/mol  BindingDB
MK1ΔH:  20.059999465942383   kJ/mol  BindingDB
MK1-TΔS:  47.2599983215332   kJ/mol  BindingDB
MK1-TΔS:  42.25   kJ/mol  BindingDB
MK1IC50:  0.36000001430511475   nM  BindingDB
MK1IC50:  10   nM  BindingDB
MK1Kd:  1.0700000524520874   nM  BindingDB
MK1Ki:  0.36000001430511475   nM  BindingDB
MK1Ki:  6.619999885559082   nM  BindingDB
MK1-TΔS:  60.22999954223633   kJ/mol  BindingDB
MK1IC50:  0.8799999952316284   nM  BindingDB
MK1ΔH:  14.630000114440918   kJ/mol  BindingDB
MK1ΔG:  49.7400016784668   kJ/mol  BindingDB
MK1ΔH:  27.59000015258789   kJ/mol  BindingDB
MK1ΔG:  48.4900016784668   kJ/mol  BindingDB
MK1Ki:  1.399999976158142   nM  BindingDB
MK1ΔH:  12.960000038146973   kJ/mol  BindingDB
MK1Kd:  5.5   nM  BindingDB
MK1ΔG:  53.5   kJ/mol  BindingDB
MK1-TΔS:  65.23999786376953   kJ/mol  BindingDB
MK1Ki:  6.900000095367432   nM  BindingDB
MK1-TΔS:  61.45000076293945   kJ/mol  BindingDB
MK1ΔG:  54.34000015258789   kJ/mol  BindingDB
MK1-TΔS:  65.6500015258789   kJ/mol  BindingDB
MK1Ki:  4.900000095367432   nM  BindingDB
MK1Ki:  0.07000000029802322   nM  BindingDB
MK1ΔG:  54.34000015258789   kJ/mol  BindingDB
MK1Ki:  2.640000104904175   nM  BindingDB
MK1ΔG:  39.709999084472656   kJ/mol  BindingDB
MK1ΔH:  31.770000457763672   kJ/mol  BindingDB
MK1ΔG:  38.459999084472656   kJ/mol  BindingDB
MK1ΔH:  2.0899999141693115   kJ/mol  BindingDB
MK1-TΔS:  30.110000610351562   kJ/mol  BindingDB
MK1-TΔS:  64.81999969482422   kJ/mol  BindingDB
MK1-TΔS:  74.02999877929688   kJ/mol  BindingDB
MK1ΔH:  15.470000267028809   kJ/mol  BindingDB
MK1Ki:  0.5199999809265137   nM  BindingDB
MK1-TΔS:  82.80000305175781   kJ/mol  BindingDB
MK1ΔG:  62.279998779296875   kJ/mol  BindingDB
MK1ΔG:  47.22999954223633   kJ/mol  BindingDB
MK1Ki:  15   nM  BindingDB
MK1Ki:  12   nM  BindingDB
MK1ΔH:  8.779999732971191   kJ/mol  BindingDB
MK1-TΔS:  57.29999923706055   kJ/mol  BindingDB
MK1ΔG:  38.869998931884766   kJ/mol  BindingDB
MK1ΔH:  6.690000057220459   kJ/mol  BindingDB
MK1Ki:  10.399999618530273   nM  BindingDB
MK1-TΔS:  65.68000030517578   kJ/mol  BindingDB
MK1ΔH:  10.029999732971191   kJ/mol  BindingDB
MK1ΔH:  15.880000114440918   kJ/mol  BindingDB
MK1-TΔS:  58.59000015258789   kJ/mol  BindingDB
MK1ΔH:  11.699999809265137   kJ/mol  BindingDB
MK1ΔH:  35.11000061035156   kJ/mol  BindingDB
MK1ΔH:  9.199999809265137   kJ/mol  BindingDB
MK1ΔH:  13.789999961853027   kJ/mol  BindingDB
MK1ΔG:  59.77000045776367   kJ/mol  BindingDB
MK1-TΔS:  61.900001525878906   kJ/mol  BindingDB
MK1Ki:  3.0999999046325684   nM  BindingDB
MK1ΔG:  51.40999984741211   kJ/mol  BindingDB
MK1ΔH:  12.119999885559082   kJ/mol  BindingDB
MK1ΔH:  14.630000114440918   kJ/mol  BindingDB
MK1ΔH:  9.199999809265137   kJ/mol  BindingDB
MK1Ki:  0.3100000023841858   nM  BindingDB
MK1ΔH:  5.019999980926514   kJ/mol  BindingDB
MK1-TΔS:  70.2699966430664   kJ/mol  BindingDB
MK1Ki:  0.6000000238418579   nM  BindingDB
MK1ΔH:  10.869999885559082   kJ/mol  BindingDB
MK1Ki:  0.3700000047683716   nM  BindingDB
MK1Ki:  0.30000001192092896   nM  BindingDB
MK1ΔH:  7.519999980926514   kJ/mol  BindingDB
MK1Ki:  0.3700000047683716   nM  BindingDB
MK1ΔH:  17.969999313354492   kJ/mol  BindingDB
MK1ΔH:  12.539999961853027   kJ/mol  BindingDB
MK1Ki:  2.809999942779541   nM  BindingDB
MK1ΔH:  10.869999885559082   kJ/mol  BindingDB
MK1ΔH:  11.699999809265137   kJ/mol  BindingDB
MK1ΔH:  12.119999885559082   kJ/mol  BindingDB
MK1ΔH:  33.439998626708984   kJ/mol  BindingDB
MK1Ki:  2   nM  BindingDB
MK1-TΔS:  59.38999938964844   kJ/mol  BindingDB
IDVKi :  3.299999952316284   nM  PDBBind
MK1Ki:  0.11999999731779099   nM  BindingDB
MK1IC50:  0.4099999964237213   nM  BindingDB
MK1Ki:  4.400000095367432   nM  BindingDB
MK1-TΔS:  65.23999786376953   kJ/mol  BindingDB
MK1-TΔS:  63.150001525878906   kJ/mol  BindingDB
MK1-TΔS:  61.900001525878906   kJ/mol  BindingDB
MK1Kd:  1.2000000476837158   nM  BindingDB
MK1-TΔS:  49.34000015258789   kJ/mol  BindingDB
MK1-TΔS:  28.860000610351562   kJ/mol  BindingDB
MK1-TΔS:  64.81999969482422   kJ/mol  BindingDB
MK1IC50:  89   nM  BindingDB
MK1ΔG:  53.09000015258789   kJ/mol  BindingDB
MK1Ki:  3.299999952316284   nM  Binding MOAD
MK1ΔG:  42.63999938964844   kJ/mol  BindingDB
MK1Ki:  0.23999999463558197   nM  BindingDB
MK1ΔH:  16.299999237060547   kJ/mol  BindingDB
MK1IC50:  1.600000023841858   nM  BindingDB
MK1IC50:  61   nM  BindingDB
MK1Ki:  7   nM  BindingDB
MK1Ki:  108   nM  BindingDB
MK1ΔG:  58.099998474121094   kJ/mol  BindingDB
MK1ΔH:  27.170000076293945   kJ/mol  BindingDB
MK1Ki:  3.109999895095825   nM  BindingDB
MK1ΔH:  8.779999732971191   kJ/mol  BindingDB
MK1-TΔS:  58.970001220703125   kJ/mol  BindingDB
MK1ΔH:  26.75   kJ/mol  BindingDB
MK1IC50:  0.6000000238418579   nM  BindingDB
MK1ΔG:  51   kJ/mol  BindingDB
MK1Kd:  1.399999976158142   nM  BindingDB
MK1Ki:  50   nM  BindingDB
MK1ΔG:  63.119998931884766   kJ/mol  BindingDB
MK1Ki:  3.0999999046325684   nM  BindingDB
MK1Ki:  40   nM  BindingDB
MK1ΔG:  44.72999954223633   kJ/mol  BindingDB
MK1Ki:  42   nM  BindingDB
MK1-TΔS:  55.630001068115234   kJ/mol  BindingDB
MK1ΔG:  62.279998779296875   kJ/mol  BindingDB
MK1-TΔS:  65.6500015258789   kJ/mol  BindingDB
MK1IC50:  370   nM  BindingDB
MK1-TΔS:  71.5   kJ/mol  BindingDB
MK1IC50:  0.5600000023841858   nM  BindingDB
MK1ΔG:  49.31999969482422   kJ/mol  BindingDB
MK1ΔH:  15.470000267028809   kJ/mol  BindingDB
MK1Ki:  0.3199999928474426   nM  BindingDB
MK1Ki:  27   nM  BindingDB
MK1IC50:  0.4000000059604645   nM  BindingDB
MK1Ki:  0.3799999952316284   nM  BindingDB
MK1ΔG:  40.54999923706055   kJ/mol  BindingDB
MK1Ki:  0.10999999940395355   nM  BindingDB
MK1ΔH:  14.630000114440918   kJ/mol  BindingDB
MK1ΔH:  15.050000190734863   kJ/mol  BindingDB
MK1ΔG:  45.13999938964844   kJ/mol  BindingDB
MK1-TΔS:  79.04000091552734   kJ/mol  BindingDB
MK1-TΔS:  52.68000030517578   kJ/mol  BindingDB
MK1-TΔS:  28.030000686645508   kJ/mol  BindingDB
MK1ΔH:  51   kJ/mol  BindingDB
MK1ΔG:  49.31999969482422   kJ/mol  BindingDB
MK1ΔH:  0   kJ/mol  BindingDB
MK1Ki:  7.599999904632568   nM  BindingDB
MK1ΔG:  60.189998626708984   kJ/mol  BindingDB
MK1ΔG:  38.459999084472656   kJ/mol  BindingDB
MK1-TΔS:  58.560001373291016   kJ/mol  BindingDB
MK1Ki:  0.5799999833106995   nM  BindingDB
MK1-TΔS:  44.75   kJ/mol  BindingDB
MK1IC50:  0.36000001430511475   nM  BindingDB
MK1ΔG:  54.7599983215332   kJ/mol  BindingDB
MK1Ki:  0.05000000074505806   nM  BindingDB
MK1IC50:  0.5899999737739563   nM  BindingDB
MK1Ki:  1.340000033378601   nM  BindingDB
MK1ΔG:  53.5   kJ/mol  BindingDB
MK1ΔG:  51   kJ/mol  BindingDB
MK1-TΔS:  62.310001373291016   kJ/mol  BindingDB
MK1ΔH:  24.65999984741211   kJ/mol  BindingDB
MK1IC50:  0.6000000238418579   nM  BindingDB
MK1ΔG:  57.68000030517578   kJ/mol  BindingDB
MK1-TΔS:  58.13999938964844   kJ/mol  BindingDB
MK1Ki:  0.2800000011920929   nM  BindingDB
MK1ΔG:  31.770000457763672   kJ/mol  BindingDB
MK1IC50:  44   nM  BindingDB
MK1-TΔS:  46.41999816894531   kJ/mol  BindingDB
MK1Ki:  0.5400000214576721   nM  BindingDB
MK1IC50:  56   nM  BindingDB
MK1-TΔS:  60.63999938964844   kJ/mol  BindingDB
MK1IC50:  52   nM  BindingDB
MK1-TΔS:  60.63999938964844   kJ/mol  BindingDB
MK1Ki:  2.700000047683716   nM  BindingDB
MK1ΔG:  43.470001220703125   kJ/mol  BindingDB
MK1ΔG:  51.83000183105469   kJ/mol  BindingDB
MK1IC50:  35   nM  BindingDB
MK1-TΔS:  59.38999938964844   kJ/mol  BindingDB
MK1Ki:  0.5400000214576721   nM  BindingDB
MK1Ki:  2.799999952316284   nM  BindingDB
MK1Ki:  0.800000011920929   nM  BindingDB
MK1Ki:  5.099999904632568   nM  BindingDB
MK1Ki:  5.099999904632568   nM  BindingDB
MK1ΔH:  18.389999389648438   kJ/mol  BindingDB
MK1ΔG:  51.83000183105469   kJ/mol  BindingDB
MK1ΔG:  50.58000183105469   kJ/mol  BindingDB
MK1IC50:  0.5899999737739563   nM  BindingDB
MK1ΔG:  43.470001220703125   kJ/mol  BindingDB
MK1Ki:  2.509999990463257   nM  BindingDB
MK1Ki:  0.550000011920929   nM  BindingDB
MK1ΔG:  47.650001525878906   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.727α = 90
b = 59.526β = 95.56
c = 87.384γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description