3O9H

Crystal Structure of wild-type HIV-1 Protease in complex with kd26

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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This is version 1.3 of the entry. See complete history. 


Literature

Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.

Nalam, M.N., Ali, A., Reddy, G.S., Cao, H., Anjum, S.G., Altman, M.D., Yilmaz, N.K., Tidor, B., Rana, T.M., Schiffer, C.A.

(2013) Chem Biol 20: 1116-1124

  • DOI: 10.1016/j.chembiol.2013.07.014
  • Primary Citation of Related Structures:  
    3O99, 3O9A, 3O9B, 3O9C, 3O9D, 3O9E, 3O9F, 3O9G, 3O9H, 3O9I

  • PubMed Abstract: 

    • The rapid evolution of HIV under selective drug pressure has led to multidrug resistant (MDR) strains that evade standard therapies. We designed highly potent HIV-1 protease inhibitors (PIs) using the substrate envelope model, which confines inhibitors within the consensus volume of natural substrates, providing inhibitors less susceptible to resistance because a mutation affecting such inhibitors will simultaneously affect viral substrate processing ...

    The rapid evolution of HIV under selective drug pressure has led to multidrug resistant (MDR) strains that evade standard therapies. We designed highly potent HIV-1 protease inhibitors (PIs) using the substrate envelope model, which confines inhibitors within the consensus volume of natural substrates, providing inhibitors less susceptible to resistance because a mutation affecting such inhibitors will simultaneously affect viral substrate processing. The designed PIs share a common chemical scaffold but utilize various moieties that optimally fill the substrate envelope, as confirmed by crystal structures. The designed PIs retain robust binding to MDR protease variants and display exceptional antiviral potencies against different clades of HIV as well as a panel of 12 drug-resistant viral strains. The substrate envelope model proves to be a powerful strategy to develop potent and robust inhibitors that avoid drug resistance.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseA, B99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: gag-pol, pol
EC: 3.4.23.16 (UniProt), 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)
UniProt
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03369 
Go to UniProtKB:  P03369
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03369
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K2E
Query on K2E
Download Ideal Coordinates CCD File 
H [auth B](3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-ethylbutyl)amino]-1-benzyl-2-hydroxypropyl}carbamate
C30 H40 N2 O9 S
ZLBAIBYBEYCDIE-KTJDEMTHSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
G [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
K2E BindingDB:  3O9H Ki: min: 8.00e-4, max: 0.1 (nM) from 2 assay(s)
PDBBind:  3O9H Ki: 8.00e-4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.735α = 90
b = 57.634β = 90
c = 61.795γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-11-23
    Changes: Structure summary
  • Version 1.2: 2013-11-27
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description