2IDW

Crystal structure analysis of HIV-1 protease mutant V82A with a potent non-peptide inhibitor (UIC-94017)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

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

  • 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 clinica ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseAB99Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: gagpol
EC: 3.4.23.16
Find proteins for Q7SSI0 (Human immunodeficiency virus 1)
Explore Q7SSI0 
Go to UniProtKB:  Q7SSI0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
017
Query on 017

Download CCD File 
B
(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
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download CCD File 
A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
017Ki:  0   nM  BindingDB
017Ki:  0.800000011920929   nM  BindingDB
017Ki:  1.100000023841858   nM  BindingDB
017EC50:  1.600000023841858   nM  BindingDB
017Ki:  2   nM  BindingDB
017EC50:  13   nM  BindingDB
017Ki:  0.009999999776482582   nM  BindingDB
017IC50:  3.799999952316284   nM  BindingDB
17Ki :  1.2999999523162842   nM  PDBBind
017Kd:  0.019999999552965164   nM  BindingDB
017Ki:  0.2199999988079071   nM  BindingDB
017IC50:  13   nM  BindingDB
017Ki:  1.2999999523162842   nM  Binding MOAD
017Ki:  0.029999999329447746   nM  BindingDB
017Ki:  0.3400000035762787   nM  BindingDB
017EC50:  112   nM  BindingDB
017Ki:  1.100000023841858   nM  BindingDB
017Ki:  0.009999999776482582   nM  BindingDB
017IC50:  0.05999999865889549   nM  BindingDB
017Ki:  0.019999999552965164   nM  BindingDB
017EC50:  0.25   nM  BindingDB
017EC50:  0.15000000596046448   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.79α = 90
b = 57.874β = 90
c = 61.939γ = 90
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
MAR345data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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