5CZB | pdb_00005czb

HCV NS5B IN COMPLEX WITH LIGAND IDX17119-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.234 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 5CZB

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Synthesis of potent and broad genotypically active NS5B HCV non-nucleoside inhibitors binding to the thumb domain allosteric site 2 of the viral polymerase.

Pierra Rouviere, C.Amador, A.Badaroux, E.Convard, T.Da Costa, D.Dukhan, D.Griffe, L.Griffon, J.F.LaColla, M.Leroy, F.Liuzzi, M.Loi, A.G.McCarville, J.Mascia, V.Milhau, J.Onidi, L.Paparin, J.L.Rahali, R.Sais, E.Seifer, M.Surleraux, D.Standring, D.Dousson, C.

(2016) Bioorg Med Chem Lett 26: 4536-4541

  • DOI: https://doi.org/10.1016/j.bmcl.2016.01.042
  • Primary Citation Related Structures: 
    5CZB

  • PubMed Abstract: 

    The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells and, as a consequence, is an attractive target for selective inhibition. This Letter describes the discovery of a new family of HCV NS5B non-nucleoside inhibitors, based on the bioisosterism between amide and phosphonamidate functions. As part of this program, SAR in this new series led to the identification of IDX17119, a potent non-nucleoside inhibitor, active on the genotypes 1b, 2a, 3a and 4a. The structure and binding domain of IDX17119 were confirmed by X-ray co-crystallization study.


  • Organizational Affiliation
    • Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France. Electronic address: claire.pierra-rouviere@merck.com.

Macromolecule Content 

  • Total Structure Weight: 129.02 kDa 
  • Atom Count: 9,819 
  • Modeled Residue Count: 1,112 
  • Deposited Residue Count: 1,126 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NS5B
A, B
563Hepatitis C virus subtype 1bMutation(s): 0 
UniProt
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Explore O92972 
Go to UniProtKB:  O92972
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO92972
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
55W

Query on 55W



Download:Ideal Coordinates CCD File
C [auth A],
U [auth B]
1-[4-(7-amino-5-methylpyrazolo[1,5-a]pyrimidin-2-yl)phenyl]-3-{[(R)-(2,4-dimethylphenyl)(methoxy)phosphoryl]amino}-1H-pyrazole-4-carboxylic acid
C26 H26 N7 O4 P
DGOTYTQLPLGHOO-KXQOOQHDSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
F [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
G [auth A]
H [auth A]
I [auth A]
AA [auth B],
BA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
CA [auth B]
DA [auth B]
EA [auth B]
K [auth A]
L [auth A]
CA [auth B],
DA [auth B],
EA [auth B],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
V [auth B]
W [auth B]
X [auth B]
D [auth A],
E [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.234 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.356α = 90
b = 108.234β = 90
c = 134.758γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-09-07
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description