4YDF

Crystal structure of compound 9 in complex with HTLV-1 Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Privileged Structures Meet Human T-Cell Leukemia Virus-1 (HTLV-1): C2-Symmetric 3,4-Disubstituted Pyrrolidines as Nonpeptidic HTLV-1 Protease Inhibitors.

Kuhnert, M.Blum, A.Steuber, H.Diederich, W.E.

(2015) J Med Chem 58: 4845-4850

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00346
  • Primary Citation of Related Structures:  
    4YDF, 4YDG

  • PubMed Abstract: 

    3,4-disubstituted pyrrolidines originally designed to inhibit the closely related HIV-1 protease were evaluated as privileged structures against HTLV-1 protease (HTLV-1 PR). The most potent inhibitor of this series exhibits two-digit nanomolar affinity and represents, to the best of our knowledge, the most potent nonpeptidic inhibitor of HTLV-1 PR described so far. The X-ray structures of two representatives bound to HTLV-1 PR were determined, and the structural basis of their affinity is discussed.


  • Organizational Affiliation

    †Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTLV-1 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4B1
Query on 4B1

Download Ideal Coordinates CCD File 
C [auth A]N-benzyl-N-[(3S,4S)-4-{benzyl[(4-nitrophenyl)sulfonyl]amino}pyrrolidin-3-yl]-3-nitrobenzenesulfonamide
C30 H29 N5 O8 S2
UIVYXDOCCSVDSG-KYJUHHDHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.35α = 90
b = 77.35β = 90
c = 160.05γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description