2GVF

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 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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
Expand
  • 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
Binding Affinity Annotations 
IDSourceBinding Affinity
NHN PDBBind:  2GVF Ki: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • 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 


Entry History 

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