Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 22.13 kDa 
• Atom Count: 2020 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

2IEO

Crystal structure analysis of HIV-1 protease mutant I84V with a potent non-peptide inhibitor (UIC-94017)

• PDB DOI: 10.2210/pdb2IEO/pdb
• Entry: 2IEO supersedes: 1S6S

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-09-19 Released: 2006-10-03 
• Deposition Author(s): Tie, Y., Boross, P.I., Wang, Y.F., Gaddis, L., Manna, D., Hussain, A.K., Leshchenko, S., Ghosh, A.K., Louis, J.M., Harrison, R.W., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.196 
• R-Value Work: 0.143 
• R-Value Observed: 0.146 

Literature

High Resolution Crystal Structures of HIV-1 Protease with a Potent Non-Peptide Inhibitor (Uic-94017) Active Against Multi-Drug-Resistant Clinical Strains.

Tie, Y., Boross, P.I., Wang, Y.F., Gaddis, L., Hussain, A.K., Leshchenko, S., Ghosh, A.K., Louis, J.M., Harrison, R.W., Weber, I.T.

(2004) J Mol Biol 338: 341-352

• PubMed: 15066436 
• DOI: 10.1016/j.jmb.2004.02.052
• Primary Citation of Related Structures:  
  2IDW, 2IEN, 2IEO


• PubMed Abstract: 
  

The compound UIC-94017 (TMC-114) is a second-generation HIV protease inhibitor with improved pharmacokinetics that is chemically related to the clinical inhibitor amprenavir. UIC-94017 is a broad-spectrum potent inhibitor active against HIV-1 clinical isolates with minimal cytotoxicity. We have determined the high-resolution crystal structures of UIC-94017 in complexes with wild-type HIV-1 protease (PR) and mutant proteases PR(V82A) and PR(I84V) that are common in drug-resistant HIV. The structures were refined at resolutions of 1.10-1.53A. The crystal structures of PR and PR(I84V) with UIC-94017 ternary complexes show that the inhibitor binds to the protease in two overlapping positions, while the PR(V82A) complex had one ordered inhibitor. In all three structures, UIC-94017 forms hydrogen bonds with the conserved main-chain atoms of Asp29 and Asp30 of the protease. These interactions are proposed to be critical for the potency of this compound against HIV isolates that are resistant to multiple protease inhibitors. Other small differences were observed in the interactions of the mutants with UIC-94017 as compared to PR. PR(V82A) showed differences in the position of the main-chain atoms of residue 82 compared to PR structure that better accommodated the inhibitor. Finally, the 1.10A resolution structure of PR(V82A) with UIC-94017 showed an unusual distribution of electron density for the catalytic aspartate residues, which is discussed in relation to the reaction mechanism.

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Organizational Affiliation: 

Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 6  Gene Names: gag, pol EC: 3.4.23.16
UniProt
Find proteins for Q7SSI0 (Human immunodeficiency virus 1) Explore Q7SSI0  Go to UniProtKB:  Q7SSI0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
017	E [auth A]	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C27 H37 N3 O7 S CJBJHOAVZSMMDJ-HEXNFIEUSA-N
CL	C [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
017	BindingDB:  2IEO	Ki: min: 2.00e-4, max: 2 (nM) from 16 assay(s)
		Kd: 0.02 (nM) from 1 assay(s)
		IC50: min: 0.06, max: 370 (nM) from 10 assay(s)
		EC50: min: 0.15, max: 112 (nM) from 5 assay(s)
	Binding MOAD:  2IEO	Ki: 3.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.196 
• R-Value Work: 0.143 
• R-Value Observed: 0.146 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.318	α = 90
b = 86.216	β = 90
c = 45.85	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
MAR345	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-09-19 
• Released Date: 2006-10-03 
Deposition Author(s): Tie, Y., Boross, P.I., Wang, Y.F., Gaddis, L., Manna, D., Hussain, A.K., Leshchenko, S., Ghosh, A.K., Louis, J.M., Harrison, R.W., Weber, I.T.
• This entry supersedes: 1S6S

Revision History  

• Version 1.0: 2006-10-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations, Structure summary