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(-) Description

Title :  HCV NS5B GT1B N316Y WITH CMPD 32
 
Authors :  S. P. Williams, K. M. Kahler, J. B. Shotwell
Date :  23 Apr 13  (Deposition) - 08 May 13  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hcv Polymerase, Hcv Ns5B, Site Iv Inhibitor, Boron, P66, P70, Rna Directed Rna Polymerase, Tar7360, Rna-Dependent Rna Polymerase, Replication-Replication Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Maynard, R. M. Crosby, B. Ellis, R. Hamatake, Z. Hong, B. A. Johns, K. M. Kahler, C. Koble, A. Leivers, M. R. Leivers, A. Mathis, A. J. Peat, J. J. Pouliot, C. D. Roberts, V. Samano, R. M. Schmidt, G. K. Smith, A. Spaltenstein, E. L. Stewart, P. Thommes, E. M. Turner, C. Voitenleitner, J. T. Walker, G. Waitt, J. Weatherhead, K. Weaver, S. Williams, L. Wright, Z. Z. Xiong, D. Haigh, J. B. Shotwell
Discovery Of A Potent Boronic Acid Derived Inhibitor Of The Hcv Rna-Dependent Rna Polymerase.
J. Med. Chem. V. 57 1902 2014
PubMed-ID: 23672667  |  Reference-DOI: 10.1021/JM400317W

(-) Compounds

Molecule 1 - HCV POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HCV POLYMERASE 1-572
    Gene: NS5B
    Mutation: YES
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 31647
    Strain: GENOTYPE 1B
    Synonym: RNA-DIRECTED RNA POLYMERASE, NS5B, P68

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
16902Ligand/Ion5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-6-[{2-[(3R)-1-HYDROXY-1,3-DIHYDRO-2,1-BENZOXABOROL-3-YL]ETHYL}(METHYLSULFONYL)AMINO]-N-METHYL-1-BENZOFURAN-3-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16901Ligand/Ion5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-6-[{2-[(3R)-1-HYDROXY-1,3-DIHYDRO-2,1-BENZOXABOROL-3-YL]ETHYL}(METHYLSULFONYL)AMINO]-N-METHYL-1-BENZOFURAN-3-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16901Ligand/Ion5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-6-[{2-[(3R)-1-HYDROXY-1,3-DIHYDRO-2,1-BENZOXABOROL-3-YL]ETHYL}(METHYLSULFONYL)AMINO]-N-METHYL-1-BENZOFURAN-3-CARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:200 , LEU A:204 , LEU A:314 , TYR A:316 , VAL A:321 , ILE A:363 , SER A:365 , CYS A:366 , SER A:368 , LEU A:384 , ASN A:411 , MET A:414 , TYR A:415 , GLN A:446 , TYR A:448 , HOH A:1017 , HOH A:1056BINDING SITE FOR RESIDUE 690 A 601
2AC2SOFTWAREARG B:200 , LEU B:204 , LEU B:314 , TYR B:316 , VAL B:321 , ILE B:363 , SER B:365 , CYS B:366 , SER B:367 , SER B:368 , LEU B:384 , ARG B:386 , MET B:414 , TYR B:415 , TYR B:448BINDING SITE FOR RESIDUE 690 B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KB7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KB7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KB7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KB7)

(-) Exons   (0, 0)

(no "Exon" information available for 4KB7)

(-) Sequences/Alignments

Asymmetric 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:545
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4kb7a_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...................hhhhhh.hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kb7 A   1 SMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGQRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKYGYGAKDVRNLSSRAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQRKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVYGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPVAGYSGGDIYHS 563
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535  ||   558     
                                                                                                                                                                             148|                                                                                                                                                                                                                                                                                                                                                                                             538|           
                                                                                                                                                                              154                                                                                                                                                                                                                                                                                                                                                                                              552           


Chain B from PDB  Type:PROTEIN  Length:548
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4kb7b_ B: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...................hhhhhh.hhh.eee.hhhhhhhhhhhh........hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................ee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kb7 B   1 SMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGQRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKYGYGAKDVRNLSSRAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQPERKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVYGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIFVAGYSGGDIYH 562
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150|      163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533     ||554        
                                                                                                                                                                               150|                                                                                                                                                                                                                                                                                                                                                                                              539|           
                                                                                                                                                                                154                                                                                                                                                                                                                                                                                                                                                                                               551
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KB7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KB7)

(-) Gene Ontology  (73, 73)

Asymmetric Unit(hide GO term definitions)

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  4kb7
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  POLG_HCVBK | P26663
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  2.7.7.48
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        POLG_HCVBK | P26663: 1a1q 1bt7 1c2p 1csj 1cu1 1gx5 1gx6 1jxp 1nhu 1nhv 1ns3 1os5 1quv 2awz 2ax0 2ax1 2brk 2brl 2dxs 2giq 2gir 2hai 2hwh 2hwi 2i1r 2jc0 2jc1 2o5d 2wcx 2who 2wrm 2xwy 2zku 3br9 3bsa 3bsc 3cde 3ciz 3cj0 3cj2 3cj3 3cj4 3cj5 3co9 3cvk 3cwj 3d28 3d5m 3e51 3fqk 3frz 3g86 3gyn 3h2l 3h59 3h5s 3h5u 3h98 3igv 3mf5 3rvb 3ua7 3udl 3vqs 4a92 4b6e 4b6f 4b71 4b73 4b74 4b75 4b76 4dgv 4dgy 4eo6 4eo8 4ih5 4ih6 4ih7 4k8b 4kai 4kbi 4ke5 4mia 4mib 4mk7 4mk8 4mk9 4mka 4mkb 4tn2 4wxp 5fps 5fpt 5fpy 8ohm

(-) Related Entries Specified in the PDB File

4kai HCV NS5B GT1B N316 WITH GSK5852A
4kbi HCV NS5B GT1B N316Y WITH CMPD 4
4ke5 HCV NS5B GT1B N316Y WITH GSK5852
4khm HCV NS5B GT1A C316 WITH GSK5852
4khr HCV NS5B GT1A C316Y WITH GSK5852