2XCF

Crystal structure of HCV NS3 protease with a boronate inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2XCF/pdb

• Classification: HYDROLASE
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-04-22 Released: 2010-06-02 
• Deposition Author(s): Li, X., Zhang, Y.-K., Liu, Y., Ding, C.Z., Li, Q., Zhou, Y., Plattner, J.J., Baker, S.J., Qian, X., Fan, D., Liao, L., Ni, Z.-J., White, G.V., Mordaunt, J.E., Lazarides, L.X., Slater, M.J., Jarvest, R.L., Thommes, P., Ellis, M., Edge, C.M., Hubbard, J.A., Nassau, P., McDowell, B., Skarzynski, T.J., Rowland, P., Somers, D.O., Kazmierski, W.M., Grimes, R.M., Wright, L.L., Smith, G.K., Zou, W., Wright, J., Pennicott, L.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Synthesis and Evaluation of Novel Alpha-Amino Cyclic Boronates as Inhibitors of Hcv Ns3 Protease.

Li, X., Zhang, Y.-K., Liu, Y., Ding, C.Z., Li, Q., Zhou, Y., Plattner, J.J., Baker, S.J., Qian, X., Fan, D., Liao, L., Ni, Z.-J., White, G.V., Mordaunt, J.E., Lazarides, L.X., Slater, M.J., Jarvest, R.L., Edge, C.M., Hubbard, J.A., Nassau, P., Mcdowell, B., Skarzynski, T.J., Thommes, P., Ellis, M., Rowland, P., Somers, D.O., Kazmierski, W.M., Grimes, R.M., Wright, L.L., Smith, G.K., Zou, W., Wright, J., Pennicott, L.E.

(2010) Bioorg Med Chem Lett 20: 3550

• PubMed: 20493689 
• DOI: https://doi.org/10.1016/j.bmcl.2010.04.129
• Primary Citation of Related Structures:  
  2XCF, 2XCN


• PubMed Abstract: 
  

  We have designed and synthesized a novel series of alpha-amino cyclic boronates and incorporated them successfully in several acyclic templates at the P1 position. These compounds are inhibitors of the HCV NS3 serine protease, and structural studies show that they inhibit the NS3 protease by trapping the Ser-139 hydroxyl group in the active site. Synthetic methodologies and SARs of this series of compounds are described.

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Organizational Affiliation: 

Anacor Pharmaceuticals, Inc., Palo Alto, CA 94303, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

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

Macromolecule Content

• Total Structure Weight: 47.6 kDa 
• Atom Count: 2,899 
• Modelled Residue Count: 370 
• Deposited Residue Count: 442 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 PROTEASE	A, B	198	Hepacivirus hominis	Mutation(s): 1
UniProt
Find proteins for C1KHN2 (Hepacivirus hominis) Explore C1KHN2  Go to UniProtKB:  C1KHN2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NS4A	C, D	23	Hepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for C9WU77 (Hepacivirus hominis) Explore C9WU77  Go to UniProtKB:  C9WU77

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BBQ	G [auth A]	CYCLOPENTYL N-[(2S)-1-[(2S,4R)-2-[[(4R)-8-HYDROXY-1,6,10-TRIOXA-5$L^{4}-BORASPIRO[4.5]DECAN-4-YL]CARBAMOYL]-4-ISOQUINOLIN-1-YLOXY-PYRROLIDIN-1-YL]-3,3-DIMETHYL-1-OXO-BUTAN-2-YL]CARBAMATE C32 H44 B N4 O9 MSXWUFQOFQGEEP-GYUKIKGESA-N
ZN	E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	F [auth A], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.889	α = 90
b = 225.889	β = 90
c = 75.196	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Li, X., Zhang, Y.-K., Liu, Y., Ding, C.Z., Li, Q., Zhou, Y., Plattner, J.J., Baker, S.J., Qian, X., Fan, D., Liao, L., Ni, Z.-J., White, G.V., Mordaunt, J.E., Lazarides, L.X., Slater, M.J., Jarvest, R.L., Thommes, P., Ellis, M., Edge, C.M., Hubbard, J.A., Nassau, P., McDowell, B., Skarzynski, T.J., Rowland, P., Somers, D.O., Kazmierski, W.M., Grimes, R.M., Wright, L.L., Smith, G.K., Zou, W., Wright, J., Pennicott, L.E.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.4: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.5: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other