Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 22.22 kDa 
• Atom Count: 1864 
• Residue Count: 198 
• Unique protein chains: 1

3D1Y

Crystal structure of HIV-1 mutant I54V and inhibitor SAQUINA

• DOI: 10.2210/pdb3D1Y/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 (BH5 ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-05-06 Released: 2008-05-27 
• Deposition Author(s): Liu, F., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 

Literature

Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.

Liu, F., Kovalevsky, A.Y., Tie, Y., Ghosh, A.K., Harrison, R.W., Weber, I.T.

(2008) J Mol Biol 381: 102-115

• PubMed: 18597780 
• DOI: 10.1016/j.jmb.2008.05.062
• Primary Citation of Related Structures:  
  3D1X, 3D1Y, 3D1Z, 3D20, 3CYW, 3CYX


• PubMed Abstract: 
  

HIV-1 (human immunodeficiency virus type 1) protease (PR) and its mutants are important antiviral drug targets. The PR flap region is critical for binding substrates or inhibitors and catalytic activity. Hence, mutations of flap residues frequently contribute to reduced susceptibility to PR inhibitors in drug-resistant HIV. Structural and kinetic analyses were used to investigate the role of flap residues Gly48, Ile50, and Ile54 in the development of drug resistance. The crystal structures of flap mutants PR(I50V) (PR with I50V mutation), PR(I54V) (PR with I54V mutation), and PR(I54M) (PR with I54M mutation) complexed with saquinavir (SQV) as well as PR(G48V) (PR with G48V mutation), PR(I54V), and PR(I54M) complexed with darunavir (DRV) were determined at resolutions of 1.05-1.40 A. The PR mutants showed changes in flap conformation, interactions with adjacent residues, inhibitor binding, and the conformation of the 80s loop relative to the wild-type PR. The PR contacts with DRV were closer in PR(G48V)-DRV than in the wild-type PR-DRV, whereas they were longer in PR(I54M)-DRV. The relative inhibition of PR(I54V) and that of PR(I54M) were similar for SQV and DRV. PR(G48V) was about twofold less susceptible to SQV than to DRV, whereas the opposite was observed for PR(I50V). The observed inhibition was in agreement with the association of G48V and I50V with clinical resistance to SQV and DRV, respectively. This analysis of structural and kinetic effects of the mutants will assist in the development of more effective inhibitors for drug-resistant HIV.

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Related Citations: 

• Ultra-High Resolution Crystal Structure of HIV-1 Protease Mutant Reveals Two Binding Sites for Clinical Inhibitor Tmc114
  Kovalevsky, A.Y., Liu, F., Leshchenko, S., Ghosh, A.K., Harrison, R.W., Weber, I.T.
  (2006) J Mol Biol 365: 901

• Kinetic, Stability, and Structural Changes in High-Resolution Crystal Structures of HIV-1 Protease with Drug-Resistant Mutations L24I, I50V, and G73S.
  Liu, F., Boross, P.I., Wang, Y.F., Tozser, J., Louis, J.M., Harrison, R.W., Weber, I.T.
  (2005) J Mol Biol 354: 789

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Organizational Affiliation: 

Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Protease	A, B	99	Human immunodeficiency virus type 1 (BH5 ISOLATE)	Mutation(s): 1  Gene Names: gag-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 P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5)) Explore P04587  Go to UniProtKB:  P04587

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ROC	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
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ROC	ΔH:  31.770000457763672   kJ/mol  BindingDB
ROC	ΔG:  55.59000015258789   kJ/mol  BindingDB
ROC	ΔH:  10.869999885559082   kJ/mol  BindingDB
ROC	Ki:  0.8999999761581421   nM  BindingDB
ROC	ΔG:  54.34000015258789   kJ/mol  BindingDB
ROC	Ki:  1.0299999713897705   nM  BindingDB
ROC	ΔG:  59.77000045776367   kJ/mol  BindingDB
ROC	-TΔS:  33.040000915527344   kJ/mol  BindingDB
ROC	Ki:  0.23000000417232513   nM  BindingDB
ROC	ΔH:  35.529998779296875   kJ/mol  BindingDB
ROC	ΔG:  43.470001220703125   kJ/mol  BindingDB
ROC	Ki:  15   nM  BindingDB
ROC	IC50:  11   nM  BindingDB
ROC	ΔH:  43.470001220703125   kJ/mol  BindingDB
ROC	ΔH:  16.299999237060547   kJ/mol  BindingDB
ROC	Ki:  0.44999998807907104   nM  BindingDB
ROC	-TΔS:  35.119998931884766   kJ/mol  BindingDB
ROC	IC50:  0.4000000059604645   nM  BindingDB
ROC	-TΔS:  61.47999954223633   kJ/mol  BindingDB
ROC	ΔH:  8.779999732971191   kJ/mol  BindingDB
ROC	ΔH:  14.630000114440918   kJ/mol  BindingDB
ROC	ΔH:  6.690000057220459   kJ/mol  BindingDB
ROC	-TΔS:  65.23999786376953   kJ/mol  BindingDB
ROC	ΔH:  17.969999313354492   kJ/mol  BindingDB
ROC	IC50:  1.7999999523162842   nM  BindingDB
ROC	ΔH:  22.56999969482422   kJ/mol  BindingDB
ROC	ΔH:  7.940000057220459   kJ/mol  BindingDB
ROC	ΔG:  49.7400016784668   kJ/mol  BindingDB
ROC	IC50:  45   nM  BindingDB
ROC	ΔG:  36.779998779296875   kJ/mol  BindingDB
ROC	ΔG:  40.130001068115234   kJ/mol  BindingDB
ROC	ΔH:  20.059999465942383   kJ/mol  BindingDB
ROC	-TΔS:  66.48999786376953   kJ/mol  BindingDB
ROC	IC50:  30   nM  BindingDB
ROC	ΔH:  30.93000030517578   kJ/mol  BindingDB
ROC	Ki:  0.20000000298023224   nM  BindingDB
ROC	ΔH:  18.389999389648438   kJ/mol  BindingDB
ROC	Ki:  2   nM  BindingDB
ROC	ΔH:  0.07999999821186066   kJ/mol  BindingDB
ROC	Ki:  0.07000000029802322   nM  BindingDB
ROC	ΔG:  60.61000061035156   kJ/mol  BindingDB
ROC	-TΔS:  59.810001373291016   kJ/mol  BindingDB
ROC	Ki:  117   nM  BindingDB
ROC	ΔG:  43.470001220703125   kJ/mol  BindingDB
ROC	-TΔS:  43.91999816894531   kJ/mol  BindingDB
ROC	ΔH:  14.630000114440918   kJ/mol  BindingDB
ROC	ΔG:  53.5   kJ/mol  BindingDB
ROC	ΔG:  35.529998779296875   kJ/mol  BindingDB
ROC	-TΔS:  80.29000091552734   kJ/mol  BindingDB
ROC	ΔG:  47.650001525878906   kJ/mol  BindingDB
ROC	IC50:  8.399999618530273   nM  BindingDB
ROC	ΔH:  40.130001068115234   kJ/mol  BindingDB
ROC	-TΔS:  60.22999954223633   kJ/mol  BindingDB
ROC	ΔG:  57.68000030517578   kJ/mol  BindingDB
ROC	-TΔS:  77.37000274658203   kJ/mol  BindingDB
ROC	-TΔS:  65.6500015258789   kJ/mol  BindingDB
ROC	ΔG:  60.61000061035156   kJ/mol  BindingDB
ROC	-TΔS:  76.94999694824219   kJ/mol  BindingDB
ROC	Kd:  0.6399999856948853   nM  BindingDB
ROC	ΔH:  15.050000190734863   kJ/mol  BindingDB
ROC	ΔH:  25.079999923706055   kJ/mol  BindingDB
ROC	-TΔS:  64.81999969482422   kJ/mol  BindingDB
ROC	ΔG:  42.63999938964844   kJ/mol  BindingDB
ROC	ΔH:  15.470000267028809   kJ/mol  BindingDB
ROC	-TΔS:  43.08000183105469   kJ/mol  BindingDB
ROC	ΔG:  62.279998779296875   kJ/mol  BindingDB
ROC	-TΔS:  28.030000686645508   kJ/mol  BindingDB
ROC	ΔG:  53.5   kJ/mol  BindingDB
ROC	ΔH:  9.199999809265137   kJ/mol  BindingDB
ROC	ΔH:  40.130001068115234   kJ/mol  BindingDB
ROC	IC50:  1   nM  BindingDB
ROC	ΔH:  15.470000267028809   kJ/mol  BindingDB
ROC	ΔG:  53.5   kJ/mol  BindingDB
ROC	Ki:  0.41999998688697815   nM  BindingDB
ROC	-TΔS:  79.04000091552734   kJ/mol  BindingDB
ROC	-TΔS:  65.6500015258789   kJ/mol  BindingDB
ROC	ΔG:  49.31999969482422   kJ/mol  BindingDB
ROC	-TΔS:  55.630001068115234   kJ/mol  BindingDB
ROC	ΔG:  61.45000076293945   kJ/mol  BindingDB
ROC	-TΔS:  61.45000076293945   kJ/mol  BindingDB
ROC	IC50:  16   nM  BindingDB
ROC	ΔG:  44.310001373291016   kJ/mol  BindingDB
ROC	ΔH:  12.539999961853027   kJ/mol  BindingDB
ROC	ΔG:  52.66999816894531   kJ/mol  BindingDB
ROC	ΔH:  12.119999885559082   kJ/mol  BindingDB
ROC	ΔG:  49.31999969482422   kJ/mol  BindingDB
ROC	-TΔS:  50.27000045776367   kJ/mol  BindingDB
ROC	ΔG:  53.5   kJ/mol  BindingDB
ROC	ΔG:  51   kJ/mol  BindingDB
ROC	-TΔS:  65.23999786376953   kJ/mol  BindingDB
ROC	Ki:  0.4300000071525574   nM  BindingDB
ROC	ΔG:  41.79999923706055   kJ/mol  BindingDB
ROC	-TΔS:  44.75   kJ/mol  BindingDB
ROC	ΔH:  12.119999885559082   kJ/mol  BindingDB
ROC	ΔH:  8.779999732971191   kJ/mol  BindingDB
ROC	ΔG:  38.040000915527344   kJ/mol  BindingDB
ROC	Ki:  0.03999999910593033   nM  BindingDB
ROC	-TΔS:  46.41999816894531   kJ/mol  BindingDB
ROC	ΔG:  56.43000030517578   kJ/mol  BindingDB
ROC	ΔH:  10.029999732971191   kJ/mol  BindingDB
ROC	-TΔS:  43.91999816894531   kJ/mol  BindingDB
ROC	-TΔS:  64.81999969482422   kJ/mol  BindingDB
ROC	Ki:  1.399999976158142   nM  BindingDB
ROC	ΔG:  55.18000030517578   kJ/mol  BindingDB
ROC	ΔH:  21.31999969482422   kJ/mol  BindingDB
ROC	ΔH:  5.019999980926514   kJ/mol  BindingDB
ROC	-TΔS:  46.84000015258789   kJ/mol  BindingDB
ROC	Ki:  89.52999877929688   nM  BindingDB
ROC	ΔG:  52.25   kJ/mol  BindingDB
ROC	-TΔS:  57.29999923706055   kJ/mol  BindingDB
ROC	-TΔS:  71.11000061035156   kJ/mol  BindingDB
ROC	Ki :  6   nM  PDBBind
ROC	Kd:  0.3100000023841858   nM  BindingDB
ROC	-TΔS:  58.59000015258789   kJ/mol  BindingDB
ROC	ΔG:  54.7599983215332   kJ/mol  BindingDB
ROC	Ki:  138   nM  BindingDB
ROC	ΔH:  13.789999961853027   kJ/mol  BindingDB
ROC	-TΔS:  58.13999938964844   kJ/mol  BindingDB
ROC	Ki:  48   nM  BindingDB
ROC	Ki:  0.46000000834465027   nM  BindingDB
ROC	-TΔS:  70.2699966430664   kJ/mol  BindingDB
ROC	-TΔS:  30.530000686645508   kJ/mol  BindingDB
ROC	Ki:  0.11999999731779099   nM  BindingDB
ROC	IC50:  1.7000000476837158   nM  BindingDB
ROC	Ki:  6   nM  Binding MOAD
ROC	Kd:  0.3199999928474426   nM  BindingDB
ROC	-TΔS:  56.86000061035156   kJ/mol  BindingDB
ROC	Ki:  1.7999999523162842   nM  BindingDB
ROC	ΔH:  25.5   kJ/mol  BindingDB
ROC	ΔH:  12.960000038146973   kJ/mol  BindingDB
ROC	Ki:  0.05999999865889549   nM  BindingDB
ROC	ΔH:  3.759999990463257   kJ/mol  BindingDB
ROC	ΔH:  12.539999961853027   kJ/mol  BindingDB
ROC	Ki:  0.1899999976158142   nM  BindingDB
ROC	-TΔS:  71.5   kJ/mol  BindingDB
ROC	Kd:  0.5799999833106995   nM  BindingDB
ROC	-TΔS:  59.38999938964844   kJ/mol  BindingDB
ROC	ΔG:  38.869998931884766   kJ/mol  BindingDB
ROC	ΔG:  41.79999923706055   kJ/mol  BindingDB
ROC	-TΔS:  57.33000183105469   kJ/mol  BindingDB
ROC	IC50:  0.4000000059604645   nM  BindingDB
ROC	Ki:  0.25   nM  BindingDB
ROC	Ki:  78.44000244140625   nM  BindingDB
ROC	IC50:  0.3400000035762787   nM  BindingDB
ROC	-TΔS:  41   kJ/mol  BindingDB
ROC	ΔH:  26.75   kJ/mol  BindingDB
ROC	ΔH:  11.699999809265137   kJ/mol  BindingDB
ROC	ΔG:  57.27000045776367   kJ/mol  BindingDB
ROC	ΔH:  8.359999656677246   kJ/mol  BindingDB
ROC	-TΔS:  75.27999877929688   kJ/mol  BindingDB
ROC	-TΔS:  74.02999877929688   kJ/mol  BindingDB
ROC	-TΔS:  61.900001525878906   kJ/mol  BindingDB
ROC	Ki:  3.700000047683716   nM  BindingDB
ROC	Ki:  0.03999999910593033   nM  BindingDB
ROC	ΔH:  27.59000015258789   kJ/mol  BindingDB
ROC	ΔG:  51.40999984741211   kJ/mol  BindingDB
ROC	ΔH:  11.699999809265137   kJ/mol  BindingDB
ROC	ΔG:  50.15999984741211   kJ/mol  BindingDB
ROC	-TΔS:  30.110000610351562   kJ/mol  BindingDB
ROC	Kd:  4.099999904632568   nM  BindingDB
ROC	-TΔS:  60.63999938964844   kJ/mol  BindingDB
ROC	ΔG:  53.09000015258789   kJ/mol  BindingDB
ROC	ΔH:  9.199999809265137   kJ/mol  BindingDB
ROC	IC50:  0.20000000298023224   nM  BindingDB
ROC	ΔG:  60.189998626708984   kJ/mol  BindingDB
ROC	-TΔS:  61.900001525878906   kJ/mol  BindingDB
ROC	Ki:  1.2999999523162842   nM  BindingDB
ROC	ΔG:  47.22999954223633   kJ/mol  BindingDB
ROC	IC50:  270   nM  BindingDB
ROC	ΔG:  45.97999954223633   kJ/mol  BindingDB
ROC	ΔG:  47.22999954223633   kJ/mol  BindingDB
ROC	IC50:  11.199999809265137   nM  BindingDB
ROC	ΔH:  9.609999656677246   kJ/mol  BindingDB
ROC	IC50:  0.23000000417232513   nM  BindingDB
ROC	ΔH:  2.0899999141693115   kJ/mol  BindingDB
ROC	-TΔS:  33.040000915527344   kJ/mol  BindingDB
ROC	Ki:  0.5199999809265137   nM  BindingDB
ROC	Ki:  0.6499999761581421   nM  BindingDB
ROC	IC50:  0.4000000059604645   nM  BindingDB
ROC	ΔG:  51.83000183105469   kJ/mol  BindingDB
ROC	ΔG:  50.58000183105469   kJ/mol  BindingDB
ROC	ΔG:  50.15999984741211   kJ/mol  BindingDB
ROC	ΔH:  35.11000061035156   kJ/mol  BindingDB

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000454 (ROC)	A	Saquinavir	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.72	α = 90
b = 85.94	β = 90
c = 46.38	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-06 
• Released Date: 2008-05-27 
Deposition Author(s): Liu, F., Weber, I.T.

Revision History 

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2013-02-27
  Changes: Other