5TWN | pdb_00005twn

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA- DEPENDENT RNA POLYMERASE IN COMPLEX WITH 5-[3-(tert-butylcarbamoyl)phenyl]-6-(ethylamino)-2-(4-fluorophenyl)-N-methylfuro[2,3-b]pyridine-3-carboxamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 
    0.223 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

The discovery of a pan-genotypic, primer grip inhibitor of HCV NS5B polymerase.

Eastman, K.J., Parcella, K., Yeung, K.S., Grant-Young, K.A., Zhu, J., Wang, T., Zhang, Z., Yin, Z., Beno, B.R., Sheriff, S., Kish, K., Tredup, J., Jardel, A.G., Halan, V., Ghosh, K., Parker, D., Mosure, K., Fang, H., Wang, Y.K., Lemm, J., Zhuo, X., Hanumegowda, U., Rigat, K., Donoso, M., Tuttle, M., Zvyaga, T., Haarhoff, Z., Meanwell, N.A., Soars, M.G., Roberts, S.B., Kadow, J.F.

(2017) Medchemcomm 8: 796-806

  • DOI: https://doi.org/10.1039/c6md00636a
  • Primary Citation Related Structures: 
    5TWM, 5TWN

  • PubMed Abstract: 

    The development of a series of novel 7-azabenzofurans exhibiting pan-genotype inhibition of HCV NS5B polymerase via binding to the primer grip site is presented. Many challenges, including poor oral bioavailability, high clearance, bioactivation, high human serum shift, and metabolic stability were encountered and overcome through SAR studies. This work culminated in the selection of BMS-986139 ( 43 ) as a preclinical candidate.

    • Organizational Affiliation: 
    • Bristol-Myers Squibb Pharmaceutical Research and Development , Department of Discovery Chemistry and Molecular Technologies , 5 Research Parkway , Wallingford , Connecticut , USA . Email: kyle.eastman@bms.com.

Macromolecule Content 

  • Total Structure Weight: 130.83 kDa 
  • Atom Count: 8,564 
  • Modeled Residue Count: 1,086 
  • Deposited Residue Count: 1,148 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NS5B RNA- DEPENDENT RNA POLYMERASE
A, B
574Hepatitis C virus (isolate Con1)Mutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1))
Explore Q9WMX2 
Go to UniProtKB:  Q9WMX2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WMX2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
23E

Query on 23E


Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]		(2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid
C38 H38 N4 O5
HDBNVTWMHMMKNY-XMHGGMMESA-N
7NG

Query on 7NG


Download:Ideal Coordinates CCD File
K [auth B]5-[3-(tert-butylcarbamoyl)phenyl]-6-(ethylamino)-2-(4-fluorophenyl)-N-methylfuro[2,3-b]pyridine-3-carboxamide
C28 H29 F N4 O3
WDGCNGHMLOOKQZ-UHFFFAOYSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free:  0.223 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66α = 90
b = 91.1β = 90
c = 233.3γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2017-03-15 
    • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Database references
  • Version 1.2: 2018-10-31
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description