2GVF | pdb_00002gvf

HCV NS3-4A protease domain complexed with a macrocyclic ketoamide inhibitor, SCH419021

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.276 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NHNClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history. 


Literature

P2-P4 macrocyclic inhibitors of hepatitis C virus NS3-4A serine protease.

Arasappan, A., Njoroge, F.G., Chen, K.X., Venkatraman, S., Parekh, T.N., Gu, H., Pichardo, J., Butkiewicz, N., Prongay, A., Madison, V., Girijavallabhan, V.

(2006) Bioorg Med Chem Lett 16: 3960-3965

  • DOI: https://doi.org/10.1016/j.bmcl.2006.05.022
  • Primary Citation of Related Structures:  
    2GVF

  • PubMed Abstract: 

    Synthesis and HCV NS3 serine protease inhibitory activity of 4-hydroxyproline derived macrocyclic inhibitors and SAR around this macrocyclic core is described in this communication. X-ray structure of inhibitor 38 bound to the protease is discussed.

    • Organizational Affiliation: 

    Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. ashok.arasappan@spcorp.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
polyprotein
A, C
199Hepacivirus hominisMutation(s): 0 
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26664
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyprotein
B, D
23N/AMutation(s): 0 
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26664
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NHN
Query on NHN
Download Ideal Coordinates CCD File 
F [auth A](6R,8S,11S)-11-CYCLOHEXYL-N-(1-{[(2-{[(1S)-2-(DIMETHYLAMINO)-2-OXO-1-PHENYLETHYL]AMINO}-2-OXOETHYL)AMINO](OXO)ACETYL}BUTYL)-10,13-DIOXO-2,5-DIOXA-9,12-DIAZATRICYCLO[14.3.1.1~6,9~]HENICOSA-1(20),16,18-TRIENE-8-CARBOXAMIDE
C42 H56 N6 O9
RJPSYFVTRHPRGV-HVHRWFTHSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.276 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.615α = 90
b = 224.615β = 90
c = 75.321γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NHNClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    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: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary