5TWM | pdb_00005twm

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 L30S 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

PDB DOI: https://doi.org/10.2210/pdb5TWM/pdb

Classification: TRANSFERASE/TRANSFERASE inhibitor
Organism(s): Hepatitis C virus JFH-1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-11-14 Released: 2017-03-15
Deposition Author(s): Sheriff, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.207 (Depositor), 0.211 (DCC)
R-Value Work:
0.169 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 30108798 Search on PubMed Search on PubMed Central
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: 65.59 kDa
Atom Count: 4,814
Modeled Residue Count: 559
Deposited Residue Count: 574
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS5B RNA-dependent RNA POLYMERASE	A	574	Hepatitis C virus JFH-1	Mutation(s): 1 Gene Names: NS5B EC: 2.7.7.48
UniProt
Find proteins for Q99IB8 (Hepatitis C virus genotype 2a (isolate JFH-1)) Explore Q99IB8 Go to UniProtKB: Q99IB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99IB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7NG Query on 7NG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PE5 Query on PE5 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C₁₈ H₃₈ O₉ CUDPPTPIUWYGFI-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.207 (Depositor), 0.211 (DCC)
R-Value Work: 0.169 (Depositor), 0.171 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.687	α = 90
b = 89.816	β = 90
c = 216.745	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
AMoRE	phasing

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
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary