Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 47.66 kDa 
• Atom Count: 2844 
• Modelled Residue Count: 371 
• Deposited Residue Count: 442 
• Unique protein chains: 2

2XNI

Protein-ligand complex of a novel macrocyclic HCV NS3 protease inhibitor derived from amino cyclic boronates

• PDB DOI: 10.2210/pdb2XNI/pdb

• Classification: HYDROLASE/HYDROLASE REGULATOR
• Organism(s): Hepacivirus C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-02 Released: 2011-08-17 
• Deposition Author(s): Li, X., Zhang, Y.-K., Liu, Y., Ding, C.Z., Zhou, Y., Li, Q., Plattner, J.J., Baker, S.J., Zhang, S., Kazmierski, W.M., Wright, L.L., Smith, G.K., Grimes, R.M., Crosby, R.M., Creech, K.L., Carballo, L.H., Slater, M.J., Jarvest, R.L., Thommes, P., Hubbard, J.A., Convery, M.A., Nassau, P.M., McDowell, W., Skarzynski, T.J., Qian, X., Fan, D., Liao, L., Ni, Z.-J., Pennicott, L.E., Zou, W., Wright, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Novel Macrocyclic Hcv Ns3 Protease Inhibitors Derived from Alpha-Amino Cyclic Boronates.

Li, X., Zhang, Y., Liu, Y., Ding, C.Z., Zhou, Y., Li, Q., Plattner, J.J., Baker, S.J., Zhang, S., Kazmierski, W.M., Wright, L.L., Smith, G.K., Grimes, R.M., Crosby, R.M., Creech, K.L., Carballo, L.H., Slater, M.J., Jarvest, R.L., Thommes, P., Hubbard, J.A., Convery, M.A., Nassau, P.M., Mcdowell, W., Skarzynski, T.J., Qian, X., Fan, D., Liao, L., Ni, Z.-J., Pennicott, L.E., Zou, W., Wright, J.

(2010) Bioorg Med Chem Lett 20: 5695

• PubMed: 20801653 
• DOI: 10.1016/j.bmcl.2010.08.022
• Primary Citation of Related Structures:  
  2XNI


• PubMed Abstract: 
  

A novel series of P2-P4 macrocyclic HCV NS3/4A protease inhibitors with α-amino cyclic boronates as warheads at the P1 site was designed and synthesized. When compared to their linear analogs, these macrocyclic inhibitors exhibited a remarkable improvement in cell-based replicon activities, with compounds 9a and 9e reaching sub-micromolar potency in replicon assay. The SAR around α-amino cyclic boronates clearly established the influence of ring size, chirality and of the substitution pattern. Furthermore, X-ray structure of the co-crystal of inhibitor 9a and NS3 protease revealed that Ser-139 in the enzyme active site traps boron in the warhead region of 9a, thus establishing its mode of action.

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Organizational Affiliation: 

Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, CA 94303, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 PROTEASE	A, B	198	Hepacivirus C	Mutation(s): 0  EC: 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958  Go to UniProtKB:  P27958

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TR8	E [auth A]	(1-{[(10-tert-butyl-15,15-dimethyl-3,9,12-trioxo-6,7,9,10,11,12,14,15,16,17,18,19,23,23a-tetradecahydro-1H,5H-2,23:5,8-dimethano-4,13,2,8,11-benzodioxatriazacyclohenicosin-7(3H)-yl)carbonyl]amino}-3-hydroxypropyl)(trihydroxy)borate(1-) C32 H52 B N4 O10 TWUMYENOHGWFCN-UHFFFAOYSA-N
ZN	F [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	G [auth A], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TR8	PDBBind:  2XNI	IC50: 43 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 233.289	α = 90
b = 233.289	β = 90
c = 78.067	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-02 
• Released Date: 2011-08-17 
Deposition Author(s): Li, X., Zhang, Y.-K., Liu, Y., Ding, C.Z., Zhou, Y., Li, Q., Plattner, J.J., Baker, S.J., Zhang, S., Kazmierski, W.M., Wright, L.L., Smith, G.K., Grimes, R.M., Crosby, R.M., Creech, K.L., Carballo, L.H., Slater, M.J., Jarvest, R.L., Thommes, P., Hubbard, J.A., Convery, M.A., Nassau, P.M., McDowell, W., Skarzynski, T.J., Qian, X., Fan, D., Liao, L., Ni, Z.-J., Pennicott, L.E., Zou, W., Wright, J.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references