3CDE	Transferase	date	Feb 26, 2008
title	Crystal Structure Of Hcv Ns5b Polymerase With A Novel Pyrida Inhibitor
authors	Q.Zhao, R.E.Showalter, Q.Han, C.R.Kissinger
compound		source
Molecule: Rna-Directed Rna Polymerase Chain: A, B Fragment: Catalytic Domain (Unp Residues 2420-2989) Ec: 2.7.7.48 Engineered: Yes Mutation: Yes		Organism_scientific: Hepatitis C Virus Strain: Genotype 1b Bk Expression_system: Escherichia Coli Expression_system_strain: Bl21(De3)Star Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21a
symmetry	Space Group: P 21 21 21	R_factor 0.191 R_Free 0.228
crystal cell	length a length b length c angle alpha angle beta angle gamma 85.637 106.258 126.930 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	N3H BindingDB	enzyme	Transferase E.C.2.7.7.48 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda(6)-benzo[1',2',4']thiadiazin-3'-yl)- 5-hydroxy-2H-pyridazin-3-ones. Part 3: Further optimization of the 2-, 6-, and 7'-substituents and initial pharmacokinetic assessments., Li LS, Zhou Y, Murphy DE, Stankovic N, Zhao J, Dragovich PS, Bertolini T, Sun Z, Ayida B, Tran CV, Ruebsam F, Webber SE, Shah AM, Tsan M, Showalter RE, Patel R, Lebrun LA, Bartkowski DM, Nolan TG, Norris DA, Kamran R, Brooks J, Sergeeva MV, Kirkovsky L, Zhao Q, Kissinger CR, Bioorg Med Chem Lett. 2008 Jun 1;18(11):3446-55. Epub 2008 Mar 5. PMID:18457949

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (188 Kb) [Save to disk] Biological Unit Coordinates (3cde.pdb1.gz) 93 Kb Biological Unit Coordinates (3cde.pdb2.gz) 93 Kb LPC: Ligand-Protein Contacts for 3CDE CSU: Contacts of Structural Units for 3CDE Likely Quarternary Molecular Structure file(s) for 3CDE Structure Factors (1642 Kb) Retrieve 3CDE in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3CDE from S2C, [Save to disk] Re-refined 3cde structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3CDE in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 3CDE

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3CDE, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3cde_B] [3cde] [3cde_A] SWISS-PROT database: [P26663] Domain organization of [POLG_HCVBK] by SWISSPFAM

Other resources with information on 3CDE

Community annotation for 3CDE at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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