1HXB

HIV-1 proteinase complexed with RO 31-8959


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere.

Krohn, A.Redshaw, S.Ritchie, J.C.Graves, B.J.Hatada, M.H.

(1991) J Med Chem 34: 3340-3342


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 PROTEASEA, B99Human immunodeficiency virus type 1 (CLONE 12)Mutation(s): 0 
Gene Names: POL
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 P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROC
Query on ROC

Download Ideal Coordinates CCD File 
C [auth A](2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide
C38 H50 N6 O5
QWAXKHKRTORLEM-UGJKXSETSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ROCKd:  0.3199999928474426   nM  BindingDB
ROCΔG:  54.34000015258789   kJ/mol  BindingDB
ROC-TΔS:  65.23999786376953   kJ/mol  BindingDB
ROCΔG:  59.77000045776367   kJ/mol  BindingDB
ROC-TΔS:  44.75   kJ/mol  BindingDB
ROCKd:  0.6399999856948853   nM  BindingDB
ROCΔG:  55.18000030517578   kJ/mol  BindingDB
ROCKi:  0.03999999910593033   nM  BindingDB
ROCΔH:  12.119999885559082   kJ/mol  BindingDB
ROC-TΔS:  58.13999938964844   kJ/mol  BindingDB
ROCKi:  0.46000000834465027   nM  BindingDB
ROCΔG:  53.5   kJ/mol  BindingDB
ROCΔG:  40.130001068115234   kJ/mol  BindingDB
ROCΔH:  12.539999961853027   kJ/mol  BindingDB
ROCΔH:  35.529998779296875   kJ/mol  BindingDB
ROCΔG:  41.79999923706055   kJ/mol  BindingDB
ROC-TΔS:  55.630001068115234   kJ/mol  BindingDB
ROCΔG:  49.31999969482422   kJ/mol  BindingDB
ROCΔG:  55.59000015258789   kJ/mol  BindingDB
ROCΔH:  17.969999313354492   kJ/mol  BindingDB
ROCKi:  0.4300000071525574   nM  BindingDB
ROCΔH:  40.130001068115234   kJ/mol  BindingDB
ROCΔG:  60.189998626708984   kJ/mol  BindingDB
ROC-TΔS:  56.86000061035156   kJ/mol  BindingDB
ROCΔH:  9.199999809265137   kJ/mol  BindingDB
ROCΔH:  13.789999961853027   kJ/mol  BindingDB
ROCKi:  0.25   nM  BindingDB
ROCΔG:  57.68000030517578   kJ/mol  BindingDB
ROC-TΔS:  35.119998931884766   kJ/mol  BindingDB
ROCKd:  0.3100000023841858   nM  BindingDB
ROCΔH:  8.359999656677246   kJ/mol  BindingDB
ROC-TΔS:  75.27999877929688   kJ/mol  BindingDB
ROC-TΔS:  66.48999786376953   kJ/mol  BindingDB
ROCΔH:  43.470001220703125   kJ/mol  BindingDB
ROCΔH:  8.779999732971191   kJ/mol  BindingDB
ROC-TΔS:  80.29000091552734   kJ/mol  BindingDB
ROC-TΔS:  79.04000091552734   kJ/mol  BindingDB
ROC-TΔS:  43.91999816894531   kJ/mol  BindingDB
ROC-TΔS:  57.29999923706055   kJ/mol  BindingDB
ROCΔG:  43.470001220703125   kJ/mol  BindingDB
ROCΔH:  16.299999237060547   kJ/mol  BindingDB
ROCΔH:  22.56999969482422   kJ/mol  BindingDB
ROCΔH:  10.029999732971191   kJ/mol  BindingDB
ROCIC50:  270   nM  BindingDB
ROCΔG:  54.7599983215332   kJ/mol  BindingDB
ROC-TΔS:  30.530000686645508   kJ/mol  BindingDB
ROCΔG:  60.61000061035156   kJ/mol  BindingDB
ROCΔG:  51   kJ/mol  BindingDB
ROCKi:  0.1899999976158142   nM  BindingDB
ROCΔH:  3.759999990463257   kJ/mol  BindingDB
ROC-TΔS:  59.38999938964844   kJ/mol  BindingDB
ROCKi:  0.11999999731779099   nM  BindingDB
ROCΔG:  47.22999954223633   kJ/mol  BindingDB
ROCΔG:  43.470001220703125   kJ/mol  BindingDB
ROC-TΔS:  76.94999694824219   kJ/mol  BindingDB
ROCΔG:  52.25   kJ/mol  BindingDB
ROCΔH:  35.11000061035156   kJ/mol  BindingDB
ROCΔG:  51.83000183105469   kJ/mol  BindingDB
ROCΔH:  0.07999999821186066   kJ/mol  BindingDB
ROCΔG:  50.58000183105469   kJ/mol  BindingDB
ROCΔH:  9.609999656677246   kJ/mol  BindingDB
ROC-TΔS:  71.5   kJ/mol  BindingDB
ROCKi:  1.7999999523162842   nM  BindingDB
ROC-TΔS:  30.110000610351562   kJ/mol  BindingDB
ROCΔH:  20.059999465942383   kJ/mol  BindingDB
ROCΔG:  43.470001220703125   kJ/mol  BindingDB
ROCKi:  0.11999999731779099   nM  Binding MOAD
ROCΔG:  38.869998931884766   kJ/mol  BindingDB
ROCKi:  1.2999999523162842   nM  BindingDB
ROCΔG:  45.97999954223633   kJ/mol  BindingDB
ROC-TΔS:  61.900001525878906   kJ/mol  BindingDB
ROCKi:  78.44000244140625   nM  BindingDB
ROCΔG:  47.22999954223633   kJ/mol  BindingDB
ROC-TΔS:  33.040000915527344   kJ/mol  BindingDB
ROC-TΔS:  60.63999938964844   kJ/mol  BindingDB
ROCIC50:  11.199999809265137   nM  BindingDB
ROCΔH:  8.779999732971191   kJ/mol  BindingDB
ROCKi:  0.05999999865889549   nM  BindingDB
ROCKi:  0.6499999761581421   nM  BindingDB
ROC-TΔS:  41   kJ/mol  BindingDB
ROCΔG:  53.09000015258789   kJ/mol  BindingDB
ROCΔH:  27.59000015258789   kJ/mol  BindingDB
ROCKd:  4.099999904632568   nM  BindingDB
ROCΔH:  31.770000457763672   kJ/mol  BindingDB
ROCΔH:  26.75   kJ/mol  BindingDB
ROCIC50:  0.4000000059604645   nM  BindingDB
ROCΔG:  50.15999984741211   kJ/mol  BindingDB
ROCΔG:  51.40999984741211   kJ/mol  BindingDB
ROCΔG:  41.79999923706055   kJ/mol  BindingDB
ROCΔH:  2.0899999141693115   kJ/mol  BindingDB
ROC-TΔS:  33.040000915527344   kJ/mol  BindingDB
ROCΔH:  10.869999885559082   kJ/mol  BindingDB
ROCIC50:  0.23000000417232513   nM  BindingDB
ROCΔG:  56.43000030517578   kJ/mol  BindingDB
ROCΔH:  5.019999980926514   kJ/mol  BindingDB
ROCΔH:  12.119999885559082   kJ/mol  BindingDB
ROCKi:  15   nM  BindingDB
ROCIC50:  11   nM  BindingDB
ROCΔG:  53.5   kJ/mol  BindingDB
ROCΔH:  12.960000038146973   kJ/mol  BindingDB
ROC-TΔS:  61.45000076293945   kJ/mol  BindingDB
ROCIC50:  0.20000000298023224   nM  BindingDB
ROCKd:  0.5799999833106995   nM  BindingDB
ROCΔH:  25.5   kJ/mol  BindingDB
ROC-TΔS:  65.6500015258789   kJ/mol  BindingDB
ROC-TΔS:  71.11000061035156   kJ/mol  BindingDB
ROCΔG:  61.45000076293945   kJ/mol  BindingDB
ROCΔH:  11.699999809265137   kJ/mol  BindingDB
ROCΔG:  50.15999984741211   kJ/mol  BindingDB
ROCΔG:  38.040000915527344   kJ/mol  BindingDB
ROCΔH:  30.93000030517578   kJ/mol  BindingDB
ROC-TΔS:  74.02999877929688   kJ/mol  BindingDB
ROCΔH:  18.389999389648438   kJ/mol  BindingDB
ROCΔH:  21.31999969482422   kJ/mol  BindingDB
ROCKi:  2   nM  BindingDB
ROCIC50:  1.7999999523162842   nM  BindingDB
ROCIC50:  0.23000000417232513   nM  BindingDB
ROCKi:  0.5199999809265137   nM  BindingDB
ROC-TΔS:  46.41999816894531   kJ/mol  BindingDB
ROCKi:  0.8999999761581421   nM  BindingDB
ROC-TΔS:  43.91999816894531   kJ/mol  BindingDB
ROCKi:  0.44999998807907104   nM  BindingDB
ROCΔH:  9.199999809265137   kJ/mol  BindingDB
ROC-TΔS:  61.47999954223633   kJ/mol  BindingDB
ROCIC50:  0.3400000035762787   nM  BindingDB
ROCIC50:  0.4000000059604645   nM  BindingDB
ROCΔH:  7.940000057220459   kJ/mol  BindingDB
ROC-TΔS:  61.900001525878906   kJ/mol  BindingDB
ROC-TΔS:  55.630001068115234   kJ/mol  BindingDB
ROCKi:  1.0299999713897705   nM  BindingDB
ROCKi:  138   nM  BindingDB
ROCKi:  0.20000000298023224   nM  BindingDB
ROCΔH:  11.699999809265137   kJ/mol  BindingDB
ROCKi:  89.52999877929688   nM  BindingDB
ROC-TΔS:  43.08000183105469   kJ/mol  BindingDB
ROCKi:  24   nM  BindingDB
ROC-TΔS:  57.33000183105469   kJ/mol  BindingDB
ROCΔG:  53.5   kJ/mol  BindingDB
ROC-TΔS:  77.37000274658203   kJ/mol  BindingDB
ROCKi:  48   nM  BindingDB
ROCΔG:  47.650001525878906   kJ/mol  BindingDB
ROCIC50:  1   nM  BindingDB
ROCIC50:  0.4000000059604645   nM  BindingDB
ROCΔH:  40.130001068115234   kJ/mol  BindingDB
ROCIC50:  16   nM  BindingDB
ROCIC50:  8.399999618530273   nM  BindingDB
ROCΔH:  25.079999923706055   kJ/mol  BindingDB
ROC-TΔS:  60.22999954223633   kJ/mol  BindingDB
ROC-TΔS:  59.810001373291016   kJ/mol  BindingDB
ROCKi:  0.41999998688697815   nM  BindingDB
ROCΔG:  57.27000045776367   kJ/mol  BindingDB
ROCKi:  3.700000047683716   nM  BindingDB
ROC-TΔS:  50.27000045776367   kJ/mol  BindingDB
ROCKi:  117   nM  BindingDB
ROCΔH:  14.630000114440918   kJ/mol  BindingDB
ROCΔH:  14.630000114440918   kJ/mol  BindingDB
ROCΔG:  35.529998779296875   kJ/mol  BindingDB
ROCΔH:  15.470000267028809   kJ/mol  BindingDB
ROCΔH:  6.690000057220459   kJ/mol  BindingDB
ROC-TΔS:  70.2699966430664   kJ/mol  BindingDB
ROC-TΔS:  65.23999786376953   kJ/mol  BindingDB
ROCΔG:  49.7400016784668   kJ/mol  BindingDB
ROCKi:  1.399999976158142   nM  BindingDB
ROCΔG:  44.310001373291016   kJ/mol  BindingDB
ROC-TΔS:  65.6500015258789   kJ/mol  BindingDB
ROCΔH:  12.539999961853027   kJ/mol  BindingDB
ROC-TΔS:  38.880001068115234   kJ/mol  BindingDB
ROCΔG:  42.63999938964844   kJ/mol  BindingDB
ROC-TΔS:  58.59000015258789   kJ/mol  BindingDB
ROCIC50:  45   nM  BindingDB
ROCΔG:  52.66999816894531   kJ/mol  BindingDB
ROCΔH:  12.119999885559082   kJ/mol  BindingDB
ROCΔH:  14.630000114440918   kJ/mol  BindingDB
ROC-TΔS:  28.030000686645508   kJ/mol  BindingDB
ROC-TΔS:  65.23999786376953   kJ/mol  BindingDB
ROC-TΔS:  46.84000015258789   kJ/mol  BindingDB
ROCIC50:  30   nM  BindingDB
ROCΔG:  49.31999969482422   kJ/mol  BindingDB
ROCΔG:  53.5   kJ/mol  BindingDB
ROCKi:  0.07000000029802322   nM  BindingDB
ROCKi:  0.15000000596046448   nM  BindingDB
ROCΔH:  15.470000267028809   kJ/mol  BindingDB
ROCΔG:  36.779998779296875   kJ/mol  BindingDB
ROC-TΔS:  64.81999969482422   kJ/mol  BindingDB
ROCKi:  0.23000000417232513   nM  BindingDB
ROCΔG:  62.279998779296875   kJ/mol  BindingDB
ROCΔH:  15.050000190734863   kJ/mol  BindingDB
ROCIC50:  1.7000000476837158   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000454 (ROC)
Query on PRD_000454
C [auth A]SaquinavirPeptide-like /  Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.31α = 90
b = 63.31β = 90
c = 83.45γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
ADSCdata collection
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    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