1YVF | pdb_00001yvf

Hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00729145

PDB DOI: https://doi.org/10.2210/pdb1YVF/pdb

Classification: TRANSFERASE
Organism(s): Orthohepacivirus hominis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-02-15 Released: 2005-04-19
Deposition Author(s): Pfefferkorn, J.A., Greene, M.L., Nugent, R.A., Gross, R.J., Mitchell, M.A., Finzel, B.C., Harris, M.S., Wells, P.A., Shelly, J.A., Anstadt, R.A., Kilkuskie, R.E., Kopta, L.A., Schwende, F.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.303 (Depositor), 0.301 (DCC)
R-Value Work:
0.240 (Depositor), 0.232 (DCC)
R-Value Observed:
0.240 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Inhibitors of HCV NS5B polymerase. Part 1: Evaluation of the southern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid.

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

(2005) Bioorg Med Chem Lett 15: 2481-2486

PubMed: 15863301 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.03.066
Primary Citation Related Structures:
1YVF

PubMed Abstract:
A novel series of nonnucleoside HCV NS5B polymerase inhibitors were prepared from (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid, a high throughput screening lead. SAR studies combined with structure based drug design focusing on the southern heterobiaryl region of the template led to the synthesis of several potent and orally bioavailable lead compounds. X-ray crystallography studies were also performed to understand the interaction of these inhibitors with HCV NS5B polymerase.

Organizational Affiliation

Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. jeffrey.a.pfefferkorn@pfizer.com

Macromolecule Content

Total Structure Weight: 65.32 kDa
Atom Count: 4,676
Modeled Residue Count: 564
Deposited Residue Count: 577
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV NS5B POLYMERASE	A	577	Orthohepacivirus hominis	Mutation(s): 0 EC: 2.7.7.48
UniProt
Find proteins for O93077 (Hepacivirus hominis) Explore O93077 Go to UniProtKB: O93077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O93077
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PH7 Query on PH7 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(2Z)-2-(BENZOYLAMINO)-3-[4-(2-BROMOPHENOXY)PHENYL]-2-PROPENOIC ACID C₂₂ H₁₆ Br N O₄ WLPJLQNKCJWAFL-RGEXLXHISA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
PH7	BindingDB: 1YVF	IC50: 100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.303 (Depositor), 0.301 (DCC)
R-Value Work: 0.240 (Depositor), 0.232 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.879	α = 90
b = 90.879	β = 90
c = 188.516	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-04-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-04-19
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: 2024-02-14
Changes: Data collection, Database references, Derived calculations