4JY1

CRYSTAL STRUCTURE OF HCV NS5B POLYMERASE IN COMPLEX WITH COMPOUND 5

PDB DOI: https://doi.org/10.2210/pdb4JY1/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Hepatitis C virus isolate HC-J4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-03-28 Released: 2014-04-23
Deposition Author(s): Coulombe, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.299
R-Value Work: 0.252

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Distinguishing drug binding pockets on proteins by complementary biophysical and biological methods

Laplante, S.R., Coulombe, R.

To be published.

Macromolecule Content

Total Structure Weight: 128.96 kDa
Atom Count: 8,731
Modelled Residue Count: 1,117
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	576	Hepatitis C virus isolate HC-J4	Mutation(s): 0 Gene Names: NS5B EC: 3.4.22 (PDB Primary Data), 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4)) Explore O92972 Go to UniProtKB: O92972
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O92972
Sequence AnnotationsExpand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NN3 Query on NN3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3-{ISOPROPYL[(TRANS-4-METHYLCYCLOHEXYL)CARBONYL]AMINO}-5-PHENYLTHIOPHENE-2-CARBOXYLIC ACID C₂₂ H₂₇ N O₃ S RZXQBIKGWSLVEK-JCNLHEQBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
NN3	BindingDB: 4JY1	Kd: min: 33, max: 427 (nM) from 2 assay(s)
NN3	BindingDB: 4JY1	IC50: min: 9, max: 2.40e+4 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.299
R-Value Work: 0.252
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.26	α = 90
b = 108.03	β = 90
c = 135.13	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-04-23

Deposition Author(s):

Coulombe, R.

Revision History (Full details and data files)

Version 1.0: 2014-04-23
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources