2YOJ | pdb_00002yoj

HCV NS5B polymerase complexed with pyridonylindole compound

• PDB DOI: https://doi.org/10.2210/pdb2YOJ/pdb

• Classification: TRANSFERASE
• Organism(s): Orthohepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-24 Released: 2013-10-09 
• Deposition Author(s): Chen, K.X., Venkatraman, S., Anilkumar, G.N., Zeng, Q., Lesburg, C.A., Vibulbhan, B., Yang, W., Velazquez, F., Chan, T.-Y., Bennett, F., Sannigrahi, M., Jiang, Y., Duca, J.S., Pinto, P., Gavalas, S., Huang, Y., Wu, W., Selyutin, O., Agrawal, S., Feld, B., Huang, H.-C., Li, C., Cheng, K.-C., Shih, N.-Y., Kozlowski, J.A., Rosenblum, S.B., Njoroge, F.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Discovery of Sch 900188: A Potent Hepatitis C Virus Ns5B Polymerase Inhibitor Prodrug as a Development Candidate

Chen, K.X., Venkatraman, S., Anilkumar, G.N., Zeng, Q., Lesburg, C.A., Vibulbhan, B., Velazquez, F., Chan, T.-Y., Bennett, F., Jiang, Y., Pinto, P., Huang, Y., Selyutin, O., Agrawal, S., Huang, H.-C., Li, C., Cheng, K.-C., Shih, N.-Y., Kozlowski, J.A., Rosenblum, S.B., Njoroge, F.G.

(2014) ACS Med Chem Lett 5: 244

• PubMed: 24900812 
• DOI: https://doi.org/10.1021/ml400192w
• Primary Citation Related Structures: 
  2YOJ


• PubMed Abstract: 
  

  Starting from indole-based hepatitis C virus (HCV) NS5B polymerase inhibitor lead compound 1, structure modifications were performed at multiple indole substituents to improve potency and pharmacokinetic (PK) properties. Bicyclic quinazolinone was found to be the best substituent at indole nitrogen, while 4,5-furanylindole was identified as the best core. Compound 11 demonstrated excellent potency. Its C2 N,N-dimethylaminoethyl ester prodrug 12 (SCH 900188) demonstrated significant improvement in PK and was selected as the development candidate.

---

Organizational Affiliation: 
• Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.

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: 132 kDa 
• Atom Count: 10,444 
• Modeled Residue Count: 1,121 
• Deposited Residue Count: 1,170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-DIRECTED RNA POLYMERASE	A, B	585	Orthohepacivirus hominis	Mutation(s): 0  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
8Y6	C [auth A], F [auth B]	4-fluoranyl-6-[(7-fluoranyl-4-oxidanylidene-3H-quinazolin-6-yl)methyl]-8-(2-oxidanylidene-1H-pyridin-3-yl)furo[2,3-e]indole-7-carboxylic acid C25 H14 F2 N4 O5 ZPEMEBKNEHMBJS-UHFFFAOYSA-N
PO4	D [auth A], E [auth A], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.271	α = 90
b = 106.227	β = 90
c = 134.553	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Chen, K.X., Venkatraman, S., Anilkumar, G.N., Zeng, Q., Lesburg, C.A., Vibulbhan, B., Yang, W., Velazquez, F., Chan, T.-Y., Bennett, F., Sannigrahi, M., Jiang, Y., Duca, J.S., Pinto, P., Gavalas, S., Huang, Y., Wu, W., Selyutin, O., Agrawal, S., Feld, B., Huang, H.-C., Li, C., Cheng, K.-C., Shih, N.-Y., Kozlowski, J.A., Rosenblum, S.B., Njoroge, F.G.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2014-06-18
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other