4YDG | pdb_00004ydg

Crystal structure of compound 10 in complex with HTLV-1 Protease

• PDB DOI: https://doi.org/10.2210/pdb4YDG/pdb

• Classification: HYDROLASE
• Organism(s): Human T-cell lymphotrophic virus type 1 (strain ATK)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-02-22 Released: 2016-02-03 
• Deposition Author(s): Kuhnert, M., Blum, A., Steuber, H., Diederich, W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.317 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.281 (Depositor) 

Starting Model: experimental

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

• PubMed: 26000468 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.92 kDa 
• Atom Count: 1,749 
• Modelled Residue Count: 219 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTLV-1 protease	A, B	116	Human T-cell lymphotrophic virus type 1 (strain ATK)	Mutation(s): 1  Gene Names: gag-pro-pol EC: 3.4.23 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for P03362 (Human T-cell leukemia virus 1 (strain Japan ATK-1 subtype A)) Explore P03362  Go to UniProtKB:  P03362

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3G	E [auth B]	N,N'-(3S,4S)-PYRROLIDINE-3,4-DIYLBIS(4-AMINO-N-BENZYLBENZENESULFONAMIDE) C30 H33 N5 O4 S2 XDDOZTWMJWWMBF-KYJUHHDHSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.317 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.281 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.61	α = 90
b = 77.61	β = 90
c = 160.23	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Kuhnert, M., Blum, A., Steuber, H., Diederich, W.E.

Revision History  

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