Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 48.08 kDa 
• Atom Count: 2937 
• Modelled Residue Count: 370 
• Deposited Residue Count: 446 
• Unique protein chains: 2

2A4R

HCV NS3 Protease Domain with a Ketoamide Inhibitor Covalently bound.

• PDB DOI: 10.2210/pdb2A4R/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Hepacivirus C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-06-29 Released: 2006-07-04 
• Deposition Author(s): Bogen, S., Saksena, A.K., Arasappan, A., Gu, H., Njoroge, F.G., Girijavallabhan, V., Pichardo, J., Butkiewicz, N., Prongay, A., Madison, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.271 
• R-Value Work: 0.201 

Literature

Hepatitis C Virus NS3-4A serine protease inhibitors: Use of a P2-P1 cyclopropyl alanine combination for improved potency.

Bogen, S., Saksena, A.K., Arasappan, A., Gu, H., Njoroge, F.G., Girijavallabhan, V., Pichardo, J., Butkiewicz, N., Prongay, A., Madison, V.

(2005) Bioorg Med Chem Lett 15: 4515-4519

• PubMed: 16112862 
• DOI: 10.1016/j.bmcl.2005.07.009
• Primary Citation of Related Structures:  
  2A4R


• PubMed Abstract: 
  

Modification of the P(2) and P(1) side chains of earlier P(3)-capped alpha-ketoamide inhibitor of HCV NS3 serine protease 1 resulted in the discovery of compound 24 with about 10-fold improvement in potency.

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Related Citations: 

• Crystal Structure of the Hepatitis C Virus NS3 Protease Domain Complexed with a Synthetic NS4a Cofactor Peptide
  Kim, J.L., Morgenstern, K.A., Lin, C., Fox, T., Dwyer, M.D., Landro, J.A., Chambers, S.P., Markland, W., Lepre, C.A., O'Malley, E.T., Harbeson, S.L., Rice, C.M., Murcko, M.A., Caron, P.R., Thomson, J.A.
  (1996) Cell 87: 343

• Hepatitis C virus NS3-4A serine protease inhibitors. SAR of P2' moiety with improved potency.
  Arasappan, A., Njoroge, F.G., Chan, T.Y., Bennett, F., Bogen, S.L., Chen, K., Gu, H., Hong, L., Jao, E., Liu, Y.T., Lovey, R.G., Parekh, T., Pike, R.E., Pinto, P., Santhanam, B., Venkatraman, S., Vaccaro, H., Wang, H., Yang, X., Zhu, Z., Mckittrick, B., Saksena, A.K., Girijavallabhan, V., Pichardo, J., Butkiewicz, N., Ingram, R., Malcolm, B., Prongay, A.J., Yao, N., Marten, B., Madison, V., Kemp, S., Levy, O., Lim-Wilby, M., Tamura, S., Ganguly, A.K.
  (2005) Bioorg Med Chem Lett 15: 4180

• The Crystal Structure of Hepatitis C Virus NS3 proteinase Reveals a Trypsin-like fold and a Structural Zinc Binding Site.
  Love, R.A., Parge, H.E., Wickersham, J.A., Hostomsky, Z., Habuka, N., Moomaw, E.W., Adachi, T., Hostomska, Z.
  (1996) Cell 87: 331

• Complex of NS3 protease and NS4a peptide of BK strain hepatitis C virus: A 2.2A resolution structure in a hexagonal crystal form.
  Yan, Y., Li, Y., Munshi, S., Sardana, V., Cole, J.L., Sardana, M., Steinkuehler, C., Tomei, L., De Francesco, R., Kuo, L.C., Chen, Z.
  (1998) Protein Sci 7: 837

• Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two protease-inhibitor complexes.
  DiMarco, S., Rizzi, M., Volpari, C., Walsh, M.A., Narjes, F., Colarusso, S., De Francesco, R., Matassa, V.G., Sollazzo, M.
  (2000) J Biol Chem 275: 7152

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Organizational Affiliation: 

Chemical Research, Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 protease/helicase	A, C	200	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 peptide	B, D	23	N/A	Mutation(s): 1
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958  Go to UniProtKB:  P27958

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNH	F [auth A]	[(N-{3-[(N-{CYCLOHEXYL[(ISOBUTOXYCARBONYL)AMINO]ACETYL}-3-CYCLOPROPYLALANYL)AMINO]-4-CYCLOPROPYL-2-OXOBUTANOYL}GLYCYL)AMINO](PHENYL)ACETIC ACID C36 H51 N5 O9 VZZMJPCOMQVXJP-ZHTHUIBPSA-N
ZN	E [auth A], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BNH	PDBBind:  2A4R	Ki: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.271 
• R-Value Work: 0.201 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 223.603	α = 90
b = 223.603	β = 90
c = 75.354	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-29 
• Released Date: 2006-07-04 
Deposition Author(s): Bogen, S., Saksena, A.K., Arasappan, A., Gu, H., Njoroge, F.G., Girijavallabhan, V., Pichardo, J., Butkiewicz, N., Prongay, A., Madison, V.

Revision History  

• Version 1.0: 2006-07-04
  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: 2021-10-20
  Changes: Database references, Derived calculations