4TYD | pdb_00004tyd

Structure-based design of a novel series of azetidine inhibitors of the hepatitis C virus NS3/4A serine protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 
    0.267 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.221 (Depositor) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4TYD

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure-based design of a novel series of azetidine inhibitors of the hepatitis C virus NS3/4A serine protease.

Parsy, C.Alexandre, F.R.Brandt, G.Caillet, C.Cappelle, S.Chaves, D.Convard, T.Derock, M.Gloux, D.Griffon, Y.Lallos, L.Leroy, F.Liuzzi, M.Loi, A.G.Moulat, L.Musiu, C.Rahali, H.Roques, V.Seifer, M.Standring, D.Surleraux, D.

(2014) Bioorg Med Chem Lett 24: 4444-4449

  • DOI: https://doi.org/10.1016/j.bmcl.2014.08.002
  • Primary Citation Related Structures: 
    4TYD

  • PubMed Abstract: 

    Structural homology between thrombin inhibitors and the early tetrapeptide HCV protease inhibitor led to the bioisosteric replacement of the P2 proline by a 2,4-disubstituted azetidine within the macrocyclic β-strand mimic. Molecular modeling guided the design of the series. This approach was validated by the excellent activity and selectivity in biochemical and cell based assays of this novel series and confirmed by the co-crystal structure of the inhibitor with the NS3/4A protein (PDB code: 4TYD).


  • Organizational Affiliation
    • IDENIX Pharmaceuticals, 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Montpellier Cedex 4, France. Electronic address: parsy.christophe@idenix.com.

Macromolecule Content 

  • Total Structure Weight: 267.73 kDa 
  • Atom Count: 17,686 
  • Modeled Residue Count: 2,321 
  • Deposited Residue Count: 2,436 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NS3 protease203Hepatitis C virus (isolate 1)Mutation(s): 1 
UniProt
Find proteins for Q0ZNA6 (Hepacivirus hominis)
Explore Q0ZNA6 
Go to UniProtKB:  Q0ZNA6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ZNA6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3EO

Query on 3EO



Download:Ideal Coordinates CCD File
DA [auth F]
IA [auth G]
KA [auth H]
N [auth A]
NA [auth J]
DA [auth F],
IA [auth G],
KA [auth H],
N [auth A],
NA [auth J],
PA [auth K],
Q [auth B],
RA [auth L],
T [auth C],
TA [auth M],
X [auth D],
Z [auth E]
(4R,6S,7Z,15S,17S)-17-[({7-methoxy-2-[4-(propan-2-yl)-1,3-thiazol-2-yl]quinolin-4-yl}oxy)methyl]-13-methyl-N-[(1-methylcyclopropyl)sulfonyl]-2,14-dioxo-1,3,13-triazatricyclo[13.2.0.0~4,6~]heptadec-7-ene-4-carboxamide
C37 H46 N6 O7 S2
DGCPGLRWAMIHKS-GYSPVFRISA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
CA [auth F]
HA [auth G]
JA [auth H]
M [auth A]
MA [auth J]
CA [auth F],
HA [auth G],
JA [auth H],
M [auth A],
MA [auth J],
OA [auth K],
P [auth B],
QA [auth L],
S [auth C],
SA [auth M],
W [auth D],
Y [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth E]
BA [auth E]
EA [auth F]
FA [auth F]
GA [auth F]
AA [auth E],
BA [auth E],
EA [auth F],
FA [auth F],
GA [auth F],
LA [auth H],
O [auth A],
R [auth B],
U [auth C],
UA [auth M],
V [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free:  0.267 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.221 (Depositor) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.691α = 90
b = 143.197β = 90
c = 240.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-09-10 
  • Deposition Author(s): Parsy, C.

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references