4JY1 | pdb_00004jy1

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 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.250 (DCC) 

Starting Model: experimental

Literature

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

Laplante, S.R., Coulombe, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NN3	C [auth A]	3-{ISOPROPYL[(TRANS-4-METHYLCYCLOHEXYL)CARBONYL]AMINO}-5-PHENYLTHIOPHENE-2-CARBOXYLIC ACID C22 H27 N O3 S RZXQBIKGWSLVEK-JCNLHEQBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NN3	BindingDB:  4JY1	Kd: min: 33, max: 427 (nM) from 2 assay(s)
		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 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.250 (DCC) 

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

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Coulombe, R.

Revision History  

• 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