3LIQ

Crystal Structure of HTLV protease complexed with the inhibitor, KNI-10673


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease.

Satoh, T.Li, M.Nguyen, J.T.Kiso, Y.Gustchina, A.Wlodawer, A.

(2010) J Mol Biol 401: 626-641

  • DOI: https://doi.org/10.1016/j.jmb.2010.06.052
  • Primary Citation of Related Structures:  
    3LIN, 3LIQ, 3LIT, 3LIV, 3LIX, 3LIY

  • PubMed Abstract: 

    Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailed study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.


  • Organizational Affiliation

    Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease
A, B
116Human T-cell leukemia virus type IMutation(s): 1 
Gene Names: prt
UniProt
Find proteins for Q82134 (Human T-cell leukemia virus type I)
Explore Q82134 
Go to UniProtKB:  Q82134
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82134
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E14
Query on E14

Download Ideal Coordinates CCD File 
C [auth B](4R)-3-[(2S,3S)-3-[[(2S)-2-[[(2S)-2-azanyl-2-phenyl-ethanoyl]amino]-3,3-dimethyl-butanoyl]amino]-2-hydroxy-4-phenyl-but anoyl]-5,5-dimethyl-N-(2-methylpropyl)-1,3-thiazolidine-4-carboxamide
C34 H49 N5 O5 S
GKUGZHJDSRCEKG-APNLASKRSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
E14 BindingDB:  3LIQ IC50: min: 331.6, max: 332 (nM) from 2 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.95α = 90
b = 77.95β = 90
c = 163.204γ = 120
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    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: 2012-12-12
    Changes: Other
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2021-10-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-09-06
    Changes: Data collection, Refinement description