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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE COMPLEX WITH BMS-791325 ALSO KNOWN AS (1AR,12BS)-8-CYCLOHEXYL-N-(DIMETHYLSULFAMOYL)-11-METHOXY-1A-{[(1R,5S)-3-METHYL-3, 8-DIAZABICYCLO[3.2.1]OCT-8-YL]CARBONYL}-1,1A,2,12B-TETRAHYDROCYCLOPROPA[D]INDOLO[2,1-A][2]BENZAZEPINE-5-CARBOXAMIDE AND 2-(4-FLUOROPHENYL)-N-METHYL-6-[(METHYLSULFONYL)AMINO]-5-(PROPAN-2-YLOXY)-1-BENZOFURAN-3-CARBOXAMIDE
 
Authors :  S. Sheriff
Date :  14 Nov 13  (Deposition) - 19 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Ns5B, Polymerase, Hcv, Hepatitis C Virus, Fingers, Palm, Thumb, Transferase/Transferase Inhibitor, Polymerase/Polymerase Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. G. Gentles, M. Ding, J. A. Bender, C. P. Bergstrom, K. Grant-Young, P. Hewawasam, T. Hudyma, S. Martin, A. Nickel, A. Regueiro-Ren, Y. Tu, Z. Yang, K. S. Yeung, X. Zheng, S. Chao, J. H. Sun, B. R. Beno, D. M. Camac, C. H. Chang, M. Gao, P. E. Morin, S. Sheriff, J. Tredup, J. Wan, M. R. Witmer, D. Xie, U. Hanumegowda, J. Knipe, K. Mosure, K. S. Santone D. D. Parker, X. Zhuo, J. Lemm, M. Liu, L. Pelosi, K. Rigat, S. Voss, Y. Wang, Y. K. Wang, R. J. Colonno, M. Gao, S. B. Roberts, Q. Gao, A. Ng, N. A. Meanwell, J. F. Kadow
Discovery And Preclinical Characterization Of The Cyclopropylindolobenzazepine Bms-791325, A Potent Allosteri Inhibitor Of The Hepatitis C Virus Ns5B Polymerase.
J. Med. Chem. V. 57 1855 2014
PubMed-ID: 24397558  |  Reference-DOI: 10.1021/JM4016894

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2420-2992
    Gene: NS5B
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 333284
    Strain: BARTENSCHLAGER
    Synonym: NS5B, P68

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
12N51Ligand/Ion2-(4-FLUOROPHENYL)-N-METHYL-6-[(METHYLSULFONYL)AMINO]-5-(PROPAN-2-YLOXY)-1-BENZOFURAN-3-CARBOXAMIDE
22N71Ligand/Ion(1AR,12BS)-8-CYCLOHEXYL-N-(DIMETHYLSULFAMOYL)-11-METHOXY-1A-{[(1R,5S)-3-METHYL-3,8-DIAZABICYCLO[3.2.1]OCT-8-YL]CARBONYL}-1,1A,2,12B-TETRAHYDROCYCLOPROPA[D]INDOLO[2,1-A][2]BENZAZEPINE-5-CARBOXAMIDE
3BOG2Ligand/IonB-OCTYLGLUCOSIDE
4SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:392 , ALA A:393 , ALA A:395 , ALA A:396 , THR A:399 , ILE A:424 , HIS A:428 , LEU A:492 , GLY A:493 , VAL A:494 , PRO A:495 , ARG A:503BINDING SITE FOR RESIDUE 2N7 A 601
2AC2SOFTWAREPHE A:193 , PRO A:197 , ARG A:200 , LEU A:204 , LEU A:314 , CYS A:316 , VAL A:321 , ILE A:363 , SER A:365 , CYS A:366 , SER A:368 , MET A:414 , TYR A:415 , TYR A:448 , HOH A:730BINDING SITE FOR RESIDUE 2N5 A 602
3AC3SOFTWAREHIS A:374 , ARG A:380 , LEU A:457 , GLY A:516 , ARG A:517BINDING SITE FOR RESIDUE SO4 A 603
4AC4SOFTWAREVAL A:499 , HIS A:502 , ARG A:503BINDING SITE FOR RESIDUE SO4 A 604
5AC5SOFTWAREGLY A:153 , ARG A:154 , ARG A:394BINDING SITE FOR RESIDUE SO4 A 605
6AC6SOFTWARETHR A:329 , ARG A:505 , VAL A:530 , ARG A:531 , THR A:532BINDING SITE FOR RESIDUE SO4 A 606
7AC7SOFTWARECYS A:146 , VAL A:147 , GLN A:148 , GLU A:150 , THR A:389 , TRP A:397 , ARG A:401 , LEU A:492BINDING SITE FOR RESIDUE BOG A 607
8AC8SOFTWARELYS A:209 , GLU A:361 , VAL A:372 , TYR A:382 , GLU A:437 , GLU A:440 , GLN A:514BINDING SITE FOR RESIDUE BOG A 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NLD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NLD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NLD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NLD)

(-) Exons   (0, 0)

(no "Exon" information available for 4NLD)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:500
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh.......hhhhhhhh....................hhhhhhhhhhhhhhhhhh......eeeeeee..............eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee...ee.....hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee....eeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nld A  54 FDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGG 558
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    || 278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558
                                                                                                                                                                                                                                                268|                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                 274
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NLD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NLD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NLD)

(-) Gene Ontology  (74, 74)

Asymmetric/Biological Unit(hide GO term definitions)

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        POLG_HCVCO | Q9WMX2: 1zh1 2jy0 2kwt 2kwz 3fql 3fqm 3fqq 3kn2 3kqh 3kqk 3kql 3kqn 3kqu 3q0z 3qgd 3qge 3qgf 3qgg 4u01 5e4f 5pzk 5pzl 5pzm 5pzn 5pzo 5pzp 5trh 5tri 5trj 5trk 5twn

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