2DXS

Crystal structure of HCV NS5B RNA polymerase complexed with a tetracyclic inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2DXS/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-08-30 Released: 2006-12-26 
• Deposition Author(s): Adachi, T., Tsuruha, J., Doi, S., Murase, K., Ikegashira, K., Watanabe, S., Uehara, K., Orita, T., Nomura, A., Kamada, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.259 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Discovery of Conformationally Constrained Tetracyclic Compounds as Potent Hepatitis C Virus NS5B RNA Polymerase Inhibitors

Ikegashira, K., Oka, T., Hirashima, S., Noji, S., Yamanaka, H., Hara, Y., Adachi, T., Tsuruha, J., Doi, S., Hase, Y., Noguchi, T., Ando, I., Ogura, N., Ikeda, S., Hashimoto, H.

(2006) J Med Chem 49: 6950-6953

• PubMed: 17125247 
• DOI: https://doi.org/10.1021/jm0610245
• Primary Citation of Related Structures:  
  2DXS


• PubMed Abstract: 
  

  We report a new series of hepatitis C virus NS5B RNA polymerase inhibitors containing a conformationally constrained tetracyclic scaffold. SAR studies led to the identification of 6,7-dihydro-5H-benzo[5,6][1,4]diazepino[7,1-a]indoles (19 and 20) bearing a basic pendent group with high biochemical and cellular potencies. These compounds displayed a very small shift in cellular potency when the replicon assay was performed in the presence of human serum albumin.

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Organizational Affiliation: 

Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 123.61 kDa 
• Atom Count: 8,690 
• Modelled Residue Count: 1,034 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	552	Hepacivirus hominis	Mutation(s): 0  Gene Names: 1B EC: 2.7.7.48
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK)) Explore P26663  Go to UniProtKB:  P26663

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JTP	C [auth A], D [auth B]	N-[(13-CYCLOHEXYL-6,7-DIHYDROINDOLO[1,2-D][1,4]BENZOXAZEPIN-10-YL)CARBONYL]-2-METHYL-L-ALANINE C27 H30 N2 O4 LNQWELVSNCYKDU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JTP	BindingDB:  2DXS	IC50: 46 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.259 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.454	α = 90
b = 67.231	β = 93.78
c = 97.853	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Adachi, T., Tsuruha, J., Doi, S., Murase, K., Ikegashira, K., Watanabe, S., Uehara, K., Orita, T., Nomura, A., Kamada, M.

Revision History  

• Version 1.0: 2006-12-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description