2F9V | pdb_00002f9v

HCV NS3 protease domain with NS4a peptide and a ketoamide inhibitor with P1 and P2 cyclopropylalannines

PDB DOI: https://doi.org/10.2210/pdb2F9V/pdb

Classification: VIRAL PROTEIN
Organism(s): Orthohepacivirus hominis, Hepatitis C virus genotype 1a (isolate H77)
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-12-06 Released: 2007-01-09
Deposition Author(s): Bogen, S.L., Ruan, S., Liu, R., Agrawal, S., Pichardo, J., Prongay, A., Baroudy, B., Saksena, A., Girijavallabhan, V., Njoroge, F.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.264 (Depositor), 0.184 (DCC)
R-Value Work:
0.189 (Depositor), 0.195 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Depeptidization efforts on P3-P2 a-ketoamide inhibitors of HCV NS3-4A serine protease: Effect on HCV replicon activity.

Bogen, S.L., Ruan, S., Liu, R., Agrawal, S., Pichardo, J., Prongay, A., Baroudy, B., Saksena, A., Girijavallabhan, V., Njoroge, F.G.

(2006) Bioorg Med Chem Lett 16: 1621-1627

PubMed: 16387495 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.12.013
Primary Citation Related Structures:
2F9V

PubMed Abstract:
Depeptidization efforts of the P(3)-P(2) region of P(3) capped alpha-ketoamide inhibitor of HCV NS3 serine protease 1 are reported. We clearly established that N-methylation of the P(2) nitrogen and modification of the P(2)' carboxylic acid terminus were essential for activity in the replicon assay.

Organizational Affiliation

Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. stephane.bogen@spcorp.com

Macromolecule Content

Total Structure Weight: 48.2 kDa
Atom Count: 2,928
Modeled Residue Count: 373
Deposited Residue Count: 448
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 protease/helicase	A, C	201	Orthohepacivirus hominis	Mutation(s): 0 Gene Names: NS3 protease domain ( residues 1027-1207 of the polyprotein).
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958 Go to UniProtKB: P27958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27958
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
polyprotein	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27958
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BN6 Query on BN6 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(2S,8R,9S,15S)-15-CYCLOHEXYL-9,12-BIS(CYCLOPROPYLMETHYL)-8-HYDROXY-20-METHYL-4,7,11,14,17-PENTAOXO-2-PHENYL-18-OXA-3,6,10,12,13,16-HEXAAZAHENICOSAN-1-OIC ACID C₃₅ H₅₂ N₆ O₉ PLFWZBVXDUFZCY-ZVVXMFRTSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C]	E [auth A], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.264 (Depositor), 0.184 (DCC)
R-Value Work: 0.189 (Depositor), 0.195 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 222.811	α = 90
b = 222.811	β = 90
c = 75.266	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
HKL-2000	data reduction
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-01-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-01-09
Type: Initial release
Version 1.1: 2008-05-01
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
Version 1.4: 2024-03-13
Changes: Data collection, Source and taxonomy, Structure summary
Version 1.5: 2024-10-16
Changes: Structure summary