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(-) Description

Title :  HCV NS5B GT1B N316Y WITH GSK5852
 
Authors :  S. P. Williams, K. M. Kahler, J. B. Shotwell
Date :  25 Apr 13  (Deposition) - 15 May 13  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
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, Polymerase, Rna Replication, 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, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
11PV4Ligand/Ion[4-({[5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-6-YL](METHYLSULFONYL)AMINO}METHYL)-2-FLUOROPHENYL]BORONIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
11PV2Ligand/Ion[4-({[5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-6-YL](METHYLSULFONYL)AMINO}METHYL)-2-FLUOROPHENYL]BORONIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
11PV2Ligand/Ion[4-({[5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-6-YL](METHYLSULFONYL)AMINO}METHYL)-2-FLUOROPHENYL]BORONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:197 , ARG 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 , MET A:414 , TYR A:415 , TYR A:448 , HOH A:978BINDING SITE FOR RESIDUE 1PV A 601
2AC2SOFTWARELEU A:419 , SER A:476 , TYR A:477 , ILE A:482 , LEU A:497 , ARG A:498 , ARG A:501 , TRP A:528 , ALA A:529 , VAL A:530 , HOH A:921 , HOH A:936 , HOH A:960 , HOH A:977BINDING SITE FOR RESIDUE 1PV A 602
3AC3SOFTWAREPRO B:197 , ARG 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:368 , LEU B:384 , MET B:414 , TYR B:415 , TYR B:448 , HOH B:775 , HOH B:955BINDING SITE FOR RESIDUE 1PV B 601
4AC4SOFTWARELEU B:419 , LEU B:474 , SER B:476 , TYR B:477 , LEU B:497 , ARG B:498 , ARG B:501 , TRP B:528 , VAL B:530 , LYS B:531 , LYS B:533 , HOH B:935 , HOH B:941 , HOH B:951 , HOH B:954BINDING SITE FOR RESIDUE 1PV B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KE5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:557 -Gly B:558

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KE5)

(-) Exons   (0, 0)

(no "Exon" information available for 4KE5)

(-) 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:548
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4ke5a_ 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..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.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
                 4ke5 A   1 SMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGQRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKYGYGAKDVRNLSSRAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQPRKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVYGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIPVAGYSGGDIYHS 563
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534     ||555        
                                                                                                                                                                              149|                                                                                                                                                                                                                                                                                                                                                                                               540|           
                                                                                                                                                                               154                                                                                                                                                                                                                                                                                                                                                                                                552           


Chain B from PDB  Type:PROTEIN  Length:547
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4ke5b_ B: 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..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ke5 B   1 SMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGQRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKYGYGAKDVRNLSSRAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQPGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVYGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIPAGYSGGDIYH 562
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       153       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      |555       
                                                                                                                                                                              149|                                                                                                                                                                                                                                                                                                                                                                                                540|         
                                                                                                                                                                               153                                                                                                                                                                                                                                                                                                                                                                                                 553
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4KE5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KE5)

(-) Gene Ontology  (73, 73)

Asymmetric Unit(hide GO term definitions)

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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 4kb7 4kbi 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 GSK5852
4kb7 HCV NS5B GT1B N316Y WITH CMPD 32
4kbi HCV NS5B GT1B N316Y WITH CMPD 4
4khm HCV NS5B GT1A WITH GSK5852
4khr HCV NS5B GT1A C316Y WITH GSK5852