Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.38 kDa 
• Atom Count: 1670 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

1HXW

HIV-1 PROTEASE DIMER COMPLEXED WITH A-84538

• DOI: 10.2210/pdb1HXW/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-01-24 Released: 1998-02-04 
• Deposition Author(s): Park, C.H., Nienaber, V., Kong, X.P.

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Experimental Data Snapshot

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

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

• PubMed: 7708670 
• DOI: 10.1073/pnas.92.7.2484
• Primary Citation of Related Structures:  
  1HXW


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A, B	99	Human immunodeficiency virus 1	Mutation(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)) Explore P12499  Go to UniProtKB:  P12499

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIT	B	RITONAVIR C37 H48 N6 O5 S2 NCDNCNXCDXHOMX-XGKFQTDJSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RIT	ΔG:  35.529998779296875   kJ/mol  BindingDB
RIT	Kd:  0.6000000238418579   nM  BindingDB
RIT	ΔG:  36.369998931884766   kJ/mol  BindingDB
RIT	ΔH:  3.759999990463257   kJ/mol  BindingDB
RIT	ΔH:  15.050000190734863   kJ/mol  BindingDB
RIT	-TΔS:  80.29000091552734   kJ/mol  BindingDB
RIT	-TΔS:  79.04000091552734   kJ/mol  BindingDB
RIT	ΔG:  57.68000030517578   kJ/mol  BindingDB
RIT	Ki:  0.11999999731779099   nM  BindingDB
RIT	Ki:  0.699999988079071   nM  BindingDB
RIT	-TΔS:  42.63999938964844   kJ/mol  BindingDB
RIT	ΔH:  40.130001068115234   kJ/mol  BindingDB
RIT	-TΔS:  52.68000030517578   kJ/mol  BindingDB
RIT	Ki:  2.4000000953674316   nM  BindingDB
RIT	Kd:  0.6100000143051147   nM  BindingDB
RIT	ΔH:  12.119999885559082   kJ/mol  BindingDB
RIT	ΔH:  10.869999885559082   kJ/mol  BindingDB
RIT	-TΔS:  56.86000061035156   kJ/mol  BindingDB
RIT	ΔG:  53.5   kJ/mol  BindingDB
RIT	Ki:  0.05999999865889549   nM  BindingDB
RIT	ΔG:  44.72999954223633   kJ/mol  BindingDB
RIT	ΔH:  12.960000038146973   kJ/mol  BindingDB
RIT	ΔG:  45.97999954223633   kJ/mol  BindingDB
RIT	ΔH:  51   kJ/mol  BindingDB
RIT	Ki:  0.15000000596046448   nM  BindingDB
RIT	Ki:  60   nM  BindingDB
RIT	ΔG:  49.31999969482422   kJ/mol  BindingDB
RIT	ΔH:  15.470000267028809   kJ/mol  BindingDB
RIT	ΔH:  35.95000076293945   kJ/mol  BindingDB
RIT	-TΔS:  69.83000183105469   kJ/mol  BindingDB
RIT	Ki:  1.2000000476837158   nM  BindingDB
RIT	-TΔS:  34.70000076293945   kJ/mol  BindingDB
RIT	ΔH:  26.75   kJ/mol  BindingDB
RIT	ΔH:  2.0899999141693115   kJ/mol  BindingDB
RIT	-TΔS:  30.110000610351562   kJ/mol  BindingDB
RIT	ΔG:  50.15999984741211   kJ/mol  BindingDB
RIT	-TΔS:  33.040000915527344   kJ/mol  BindingDB
RIT	-TΔS:  65.6500015258789   kJ/mol  BindingDB
RIT	ΔH:  15.470000267028809   kJ/mol  BindingDB
RIT	Ki:  0.019999999552965164   nM  BindingDB
RIT	Ki:  0.015000000596046448   nM  Binding MOAD
RIT	ΔG:  33.439998626708984   kJ/mol  BindingDB
RIT	-TΔS:  46.41999816894531   kJ/mol  BindingDB
RIT	-TΔS:  43.91999816894531   kJ/mol  BindingDB
RIT	Ki:  0.800000011920929   nM  BindingDB
RIT	ΔG:  54.7599983215332   kJ/mol  BindingDB
RIT	IC50:  67   nM  BindingDB
RIT	-TΔS:  60.63999938964844   kJ/mol  BindingDB
RIT	ΔG:  60.189998626708984   kJ/mol  BindingDB
RIT	ΔG:  43.470001220703125   kJ/mol  BindingDB
RIT	ΔG:  56.0099983215332   kJ/mol  BindingDB
RIT	ΔG:  56.43000030517578   kJ/mol  BindingDB
RIT	ΔG:  51.83000183105469   kJ/mol  BindingDB
RIT	ΔG:  38.040000915527344   kJ/mol  BindingDB
RIT	ΔG:  52.25   kJ/mol  BindingDB
RIT	-TΔS:  43.91999816894531   kJ/mol  BindingDB
RIT	ΔG:  55.18000030517578   kJ/mol  BindingDB
RIT	ΔH:  40.130001068115234   kJ/mol  BindingDB
RIT	Ki:  32   nM  BindingDB
RIT	Ki:  0.9100000262260437   nM  BindingDB
RIT	Ki:  1.100000023841858   nM  BindingDB
RIT	-TΔS:  76.94999694824219   kJ/mol  BindingDB
RIT	ΔG:  31.770000457763672   kJ/mol  BindingDB
RIT	Ki:  109   nM  BindingDB
RIT	Ki:  0.019999999552965164   nM  BindingDB
RIT	-TΔS:  58.560001373291016   kJ/mol  BindingDB
RIT	ΔH:  22.56999969482422   kJ/mol  BindingDB
RIT	Ki:  0.23000000417232513   nM  BindingDB
RIT	Ki:  0.46000000834465027   nM  BindingDB
RIT	ΔH:  73.1500015258789   kJ/mol  BindingDB
RIT	ΔH:  0   kJ/mol  BindingDB
RIT	ΔG:  28.84000015258789   kJ/mol  BindingDB
RIT	-TΔS:  58.59000015258789   kJ/mol  BindingDB
RIT	-TΔS:  30.110000610351562   kJ/mol  BindingDB
RIT	Ki :  0.015000000596046448   nM  PDBBind
RIT	ΔG:  38.869998931884766   kJ/mol  BindingDB
RIT	ΔH:  4.599999904632568   kJ/mol  BindingDB
RIT	-TΔS:  57.33000183105469   kJ/mol  BindingDB
RIT	-TΔS:  46.84000015258789   kJ/mol  BindingDB
RIT	ΔG:  53.5   kJ/mol  BindingDB
RIT	ΔH:  5.019999980926514   kJ/mol  BindingDB
RIT	ΔH:  9.199999809265137   kJ/mol  BindingDB
RIT	ΔH:  24.239999771118164   kJ/mol  BindingDB
RIT	ΔH:  30.510000228881836   kJ/mol  BindingDB
RIT	ΔH:  12.960000038146973   kJ/mol  BindingDB
RIT	Ki:  0.029999999329447746   nM  BindingDB
RIT	ΔH:  9.609999656677246   kJ/mol  BindingDB
RIT	-TΔS:  43.08000183105469   kJ/mol  BindingDB
RIT	ΔG:  45.13999938964844   kJ/mol  BindingDB
RIT	-TΔS:  75.27999877929688   kJ/mol  BindingDB
RIT	-TΔS:  44.75   kJ/mol  BindingDB
RIT	ΔH:  13.789999961853027   kJ/mol  BindingDB
RIT	Ki:  0.20000000298023224   nM  BindingDB
RIT	ΔH:  12.539999961853027   kJ/mol  BindingDB
RIT	Ki:  30   nM  BindingDB
RIT	ΔH:  43.470001220703125   kJ/mol  BindingDB
RIT	-TΔS:  76.54000091552734   kJ/mol  BindingDB
RIT	ΔH:  27.59000015258789   kJ/mol  BindingDB
RIT	ΔG:  41.79999923706055   kJ/mol  BindingDB
RIT	ΔG:  53.5   kJ/mol  BindingDB
RIT	ΔG:  49.31999969482422   kJ/mol  BindingDB
RIT	-TΔS:  42.25   kJ/mol  BindingDB
RIT	ΔG:  42.63999938964844   kJ/mol  BindingDB
RIT	-TΔS:  45.59000015258789   kJ/mol  BindingDB
RIT	Ki:  0.5   nM  BindingDB
RIT	ΔG:  40.959999084472656   kJ/mol  BindingDB
RIT	ΔG:  39.709999084472656   kJ/mol  BindingDB
RIT	Ki:  0.3700000047683716   nM  BindingDB
RIT	Ki:  98   nM  BindingDB
RIT	-TΔS:  102.05999755859375   kJ/mol  BindingDB
RIT	IC50:  9850   nM  BindingDB
RIT	ΔH:  12.119999885559082   kJ/mol  BindingDB
RIT	-TΔS:  64.81999969482422   kJ/mol  BindingDB
RIT	EC50:  150   nM  BindingDB
RIT	Ki:  15   nM  BindingDB
RIT	-TΔS:  65.23999786376953   kJ/mol  BindingDB
RIT	Ki:  23   nM  BindingDB
RIT	ΔH:  21.739999771118164   kJ/mol  BindingDB
RIT	ΔH:  8.779999732971191   kJ/mol  BindingDB
RIT	ΔG:  36.779998779296875   kJ/mol  BindingDB
RIT	ΔG:  34.279998779296875   kJ/mol  BindingDB
RIT	-TΔS:  50.27000045776367   kJ/mol  BindingDB
RIT	ΔH:  25.079999923706055   kJ/mol  BindingDB
RIT	ΔG:  52.66999816894531   kJ/mol  BindingDB
RIT	ΔG:  53.91999816894531   kJ/mol  BindingDB
RIT	ΔG:  57.27000045776367   kJ/mol  BindingDB
RIT	-TΔS:  36.369998931884766   kJ/mol  BindingDB
RIT	ΔG:  45.560001373291016   kJ/mol  BindingDB
RIT	ΔG:  44.310001373291016   kJ/mol  BindingDB
RIT	ΔG:  54.34000015258789   kJ/mol  BindingDB
RIT	Ki:  0.699999988079071   nM  BindingDB
RIT	Ki:  40   nM  BindingDB
RIT	ΔG:  55.59000015258789   kJ/mol  BindingDB
RIT	ΔH:  14.630000114440918   kJ/mol  BindingDB
RIT	Ki:  3.0999999046325684   nM  BindingDB
RIT	ΔG:  40.130001068115234   kJ/mol  BindingDB
RIT	-TΔS:  51.0099983215332   kJ/mol  BindingDB
RIT	Ki:  4   nM  BindingDB
RIT	Ki:  13   nM  BindingDB
RIT	ΔH:  0.07999999821186066   kJ/mol  BindingDB
RIT	ΔH:  12.960000038146973   kJ/mol  BindingDB
RIT	-TΔS:  57.29999923706055   kJ/mol  BindingDB
RIT	ΔG:  49.7400016784668   kJ/mol  BindingDB
RIT	ΔH:  17.969999313354492   kJ/mol  BindingDB
RIT	ΔH:  11.699999809265137   kJ/mol  BindingDB
RIT	-TΔS:  70.2699966430664   kJ/mol  BindingDB
RIT	ΔG:  40.54999923706055   kJ/mol  BindingDB
RIT	-TΔS:  62.7599983215332   kJ/mol  BindingDB
RIT	Ki:  3.0199999809265137   nM  BindingDB
RIT	ΔH:  17.559999465942383   kJ/mol  BindingDB
RIT	Ki:  0.3700000047683716   nM  BindingDB
RIT	ΔH:  2.930000066757202   kJ/mol  BindingDB
RIT	-TΔS:  66.48999786376953   kJ/mol  BindingDB
RIT	-TΔS:  82.80000305175781   kJ/mol  BindingDB
RIT	ΔG:  45.560001373291016   kJ/mol  BindingDB
RIT	ΔH:  11.699999809265137   kJ/mol  BindingDB
RIT	-TΔS:  70.2699966430664   kJ/mol  BindingDB
RIT	-TΔS:  39.29999923706055   kJ/mol  BindingDB
RIT	Ki:  4.5   nM  BindingDB
RIT	Ki:  0.05999999865889549   nM  BindingDB
RIT	-TΔS:  43.08000183105469   kJ/mol  BindingDB
RIT	Ki:  0.5899999737739563   nM  BindingDB
RIT	ΔH:  33.439998626708984   kJ/mol  BindingDB
RIT	-TΔS:  35.540000915527344   kJ/mol  BindingDB
RIT	ΔH:  12.119999885559082   kJ/mol  BindingDB
RIT	ΔH:  43.470001220703125   kJ/mol  BindingDB
RIT	Ki:  2.809999942779541   nM  BindingDB
RIT	ΔH:  8.359999656677246   kJ/mol  BindingDB

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001001 (RIT)	B	RITONAVIR	Peptide-like /  Inhibitor		--

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 = 61.06	α = 90
b = 86.88	β = 90
c = 46.62	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
R-AXIS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-01-24 
• Released Date: 1998-02-04 
Deposition Author(s): Park, C.H., Nienaber, V., Kong, X.P.

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