4TLR | pdb_00004tlr

NS5b in complex with lactam-thiophene carboxylic acids

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Design and synthesis of lactam-thiophene carboxylic acids as potent hepatitis C virus polymerase inhibitors.

Barnes-Seeman, D., Boiselle, C., Capacci-Daniel, C., Chopra, R., Hoffmaster, K., Jones, C.T., Kato, M., Lin, K., Ma, S., Pan, G., Shu, L., Wang, J., Whiteman, L., Xu, M., Zheng, R., Fu, J.

(2014) Bioorg Med Chem Lett 24: 3979-3985

  • DOI: https://doi.org/10.1016/j.bmcl.2014.06.031
  • Primary Citation Related Structures: 
    4TLR, 4TN2

  • PubMed Abstract: 

    Herein we report the successful incorporation of a lactam as an amide replacement in the design of hepatitis C virus NS5B Site II thiophene carboxylic acid inhibitors. Optimizing potency in a replicon assay and minimizing potential risk for CYP3A4 induction led to the discovery of inhibitor 22a. This lead compound has a favorable pharmacokinetic profile in rats and dogs.

    • Organizational Affiliation: 
    • Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, United States.

Macromolecule Content 

  • Total Structure Weight: 65.33 kDa 
  • Atom Count: 4,993 
  • Modeled Residue Count: 564 
  • Deposited Residue Count: 578 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NS5b578Hepatitis C virus (isolate 1)Mutation(s): 0 
EC: 2.7.7.48

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
33H

Query on 33H


Download:Ideal Coordinates CCD File
B [auth A]3-{(2R,5R)-5-cyclohexyl-2-[(2R)-2-hydroxypropyl]-3-oxomorpholin-4-yl}-5-(3,3-dimethylbut-1-yn-1-yl)thiophene-2-carboxylic acid
C24 H33 N O5 S
HBHITDKHOXLFLK-UIAACRFSSA-N
79Z

Query on 79Z


Download:Ideal Coordinates CCD File
C [auth A]5-cyclopropyl-2-(4-fluorophenyl)-6-[(2-hydroxyethyl)(methylsulfonyl)amino]-N-methyl-1-benzofuran-3-carboxamide
C22 H23 F N2 O5 S
WTDWVLJJJOTABN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.41α = 90
b = 68.06β = 90
c = 143.72γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
BUSTERrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2014-12-10 
    • Deposition Author(s): Chopra, R.

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Derived calculations
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.5: 2024-11-13
    Changes: Structure summary