4MZ4 | pdb_00004mz4

Discovery of an Irreversible HCV NS5B Polymerase Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4MZ4/pdb

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


• Deposited: 2013-09-29 Released: 2013-12-11 
• Deposition Author(s): Zeng, Q., Anilkumar, G.N., Rosenblum, S.B., Huang, H.-C., Lesburg, C.A., Jiang, Y., Selyutin, O., Chan, T.-Y., Bennett, F., Chen, K.X., Venkatraman, S., Sannigrahi, M., Velazquez, F., Duca, J.S., Gavalas, S., Huang, Y., Pu, H., Wang, L., Pinto, P., Vibulbhan, B., Agrawal, S., Ferrari, E., Jiang, C.-K., Li, C., Hesk, D., Gesell, J., Sorota, S., Shih, N.-Y., Njoroge, F.G., Kozlowski, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.204 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Discovery of an irreversible HCV NS5B polymerase inhibitor.

Zeng, Q., Nair, A.G., Rosenblum, S.B., Huang, H.C., Lesburg, C.A., Jiang, Y., Selyutin, O., Chan, T.Y., Bennett, F., Chen, K.X., Venkatraman, S., Sannigrahi, M., Velazquez, F., Duca, J.S., Gavalas, S., Huang, Y., Pu, H., Wang, L., Pinto, P., Vibulbhan, B., Agrawal, S., Ferrari, E., Jiang, C.K., Li, C., Hesk, D., Gesell, J., Sorota, S., Shih, N.Y., Njoroge, F.G., Kozlowski, J.A.

(2013) Bioorg Med Chem Lett 23: 6585-6587

• PubMed: 24252545 
• DOI: https://doi.org/10.1016/j.bmcl.2013.10.060
• Primary Citation Related Structures: 
  4MZ4


• PubMed Abstract: 
  

  The discovery of lead compound 2e was described. Its covalent binding to HCV NS5B polymerase enzyme was investigated by X-ray analysis. The results of distribution, metabolism and pharmacokinetics were reported. Compound 2e was demonstrated to be potent (replicon GT-1b EC50 = 0.003 μM), highly selective, and safe in in vitro and in vivo assays.

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Organizational Affiliation: 
• Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.

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: 129.59 kDa 
• Atom Count: 10,615 
• Modeled Residue Count: 1,123 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, B	576	Hepatitis C virus isolate HC-J4	Mutation(s): 0  Gene Names: NS5B EC: 2.7.7.48
UniProt
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4)) Explore O92972  Go to UniProtKB:  O92972

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2F3	C [auth A], G [auth B]	1-[(2-chloroquinolin-3-yl)methyl]-6-fluoro-5-methyl-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid C25 H17 Cl F N3 O3 UZVPIJMLVISXHS-UHFFFAOYSA-N
PO4	D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.204 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.986	α = 90
b = 106.596	β = 90
c = 134.602	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Zeng, Q., Anilkumar, G.N., Rosenblum, S.B., Huang, H.-C., Lesburg, C.A., Jiang, Y., Selyutin, O., Chan, T.-Y., Bennett, F., Chen, K.X., Venkatraman, S., Sannigrahi, M., Velazquez, F., Duca, J.S., Gavalas, S., Huang, Y., Pu, H., Wang, L., Pinto, P., Vibulbhan, B., Agrawal, S., Ferrari, E., Jiang, C.-K., Li, C., Hesk, D., Gesell, J., Sorota, S., Shih, N.-Y., Njoroge, F.G., Kozlowski, J.A.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2013-12-18
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary