4U01

HCV NS3/4A serine protease in complex with 6570


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and structural diversity of the hepatitis C virus NS3/4A serine protease inhibitor series leading to clinical candidate IDX320.

Parsy, C.C.Alexandre, F.R.Bidau, V.Bonnaterre, F.Brandt, G.Caillet, C.Cappelle, S.Chaves, D.Convard, T.Derock, M.Gloux, D.Griffon, Y.Lallos, L.B.Leroy, F.Liuzzi, M.Loi, A.G.Moulat, L.Chiara, M.Rahali, H.Roques, V.Rosinovsky, E.Savin, S.Seifer, M.Standring, D.Surleraux, D.

(2015) Bioorg Med Chem Lett 25: 5427-5436

  • DOI: 10.1016/j.bmcl.2015.09.009
  • Primary Citation of Related Structures:  
    4U01

  • PubMed Abstract: 
  • Exploration of the P2 region by mimicking the proline motif found in BILN2061 resulted in the discovery of two series of potent HCV NS3/4A protease inhibitors. X-ray crystal structure of the ligand in contact with the NS3/4A protein and modulation of the quinoline heterocyclic region by structure based design and modeling allowed for the optimization of enzyme potency and cellular activity ...

    Exploration of the P2 region by mimicking the proline motif found in BILN2061 resulted in the discovery of two series of potent HCV NS3/4A protease inhibitors. X-ray crystal structure of the ligand in contact with the NS3/4A protein and modulation of the quinoline heterocyclic region by structure based design and modeling allowed for the optimization of enzyme potency and cellular activity. This research led to the selection of clinical candidate IDX320 having good genotype coverage and pharmacokinetic properties in various species.


    Organizational Affiliation

    IDENIX, a wholly-owned subsidiary of Merck & Co, 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Montpellier Cedex 4, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural 3 protease
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I [auth J]
203Hepatitis C virus (isolate Con1)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 Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1))
Explore Q9WMX2 
Go to UniProtKB:  Q9WMX2
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NS4A protein16Hepacivirus CMutation(s): 0 
Gene Names: NS4A
UniProt
Find proteins for F0UY39 (Hepacivirus C)
Explore F0UY39 
Go to UniProtKB:  F0UY39
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
39W (Subject of Investigation/LOI)
Query on 39W

Download Ideal Coordinates CCD File 
CA [auth E] , FA [auth F] , HA [auth G] , KA [auth H] , MA [auth J] , S [auth A] , U [auth B] , X [auth C] , 
CA [auth E], FA [auth F], HA [auth G], KA [auth H], MA [auth J], S [auth A], U [auth B], X [auth C], Z [auth D]
(2S,3aS,10Z,11aS,12aR)-2-({8-fluoro-7-methoxy-2-[4-(propan-2-yl)-1,3-thiazol-2-yl]quinolin-4-yl}oxy)-5-methyl-N-[(1-methylcyclopropyl)sulfonyl]-4,14-dioxo-1,2,3,3a,4,5,6,7,8,9,11a,12,13,14-tetradecahydro-12aH-cyclopropa[m]pyrrolo[1,2-c][1,3,6]triazacyclotetradecine-12a-carboxamide
C37 H45 F N6 O7 S2
WCUAGYIETHEUQO-MULYSJGUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D] , DA [auth E] , GA [auth F] , IA [auth G] , LA [auth H] , NA [auth J] , T [auth A] , V [auth B] , 
AA [auth D], DA [auth E], GA [auth F], IA [auth G], LA [auth H], NA [auth J], T [auth A], V [auth B], Y [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth D], EA [auth E], JA [auth G], W [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.034α = 90
b = 174.363β = 90
c = 133.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2015-11-11
    Changes: Database references