1Z4U | pdb_00001z4u

hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00799585

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.265 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 

Literature

Inhibitors of HCV NS5B polymerase. Part 2: Evaluation of the northern region of (2Z)-2-benzoylamino-3-(4-phenoxy-phenyl)-acrylic acid

Pfefferkorn, J.A., Nugent, R., Gross, R.J., Greene, M., Mitchell, M.A., Reding, M.T., Funk, L.A., Anderson, R., Wells, P.A., Shelly, J.A., Anstadt, R., Finzel, B.C., Harris, M.S., Kilkuskie, R.E., Kopta, L.A., Schwende, F.J.

(2005) Bioorg Med Chem Lett 15: 2812-2818

  • DOI: https://doi.org/10.1016/j.bmcl.2005.03.106
  • Primary Citation Related Structures: 
    1Z4U

  • PubMed Abstract: 

    A novel series of non-nucleoside HCV NS5B polymerase inhibitors was prepared from a (2Z)-2-benzoylamino-3-(4-phenoxy-phenyl)-acrylic acid template. Solution and solid phase analog synthesis focused on the northern region of the template combined with structure based design led to the discovery of several potent and orally bioavailable lead compounds.

    • Organizational Affiliation: 
    • Pfizer Global Research & Development, Michigan Laboratories, Ann Arbor, 48105, USA. jeffrey.a.pfefferkorn@pfizer.com

Macromolecule Content 

  • Total Structure Weight: 65.29 kDa 
  • Atom Count: 4,604 
  • Modeled Residue Count: 564 
  • Deposited Residue Count: 577 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HCV NS5B POLYMERASE577Orthohepacivirus hominisMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for O93077 (Hepacivirus hominis)
Explore O93077 
Go to UniProtKB:  O93077
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93077
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PH9

Query on PH9


Download:Ideal Coordinates CCD File
D [auth A](2Z)-2-[(1-ADAMANTYLCARBONYL)AMINO]-3-[4-(2-BROMOPHENOXY)PHENYL]PROP-2-ENOIC ACID
C26 H28 Br N O4
SJHUUZUNPUEALW-ZDXWGTOVSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL


Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.265 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.344α = 90
b = 91.344β = 90
c = 189.111γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2024-04-03
    Changes: Advisory, Atomic model