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(-) Description

Title :  DISCOVERY OF AN IRREVERSIBLE HCV NS5B POLYMERASE INHIBITOR
 
Authors :  Q. Zeng, G. N. Anilkumar, S. B. Rosenblum, H. -C. Huang, C. A. Lesburg, Y. O. Selyutin, T. -Y. Chan, F. Bennett, K. X. Chen, S. Venkatraman, M. San F. Velazquez, J. S. Duca, S. Gavalas, Y. Huang, H. Pu, L. Wang, P. Pinto, B. Vibulbhan, S. Agrawal, E. Ferrari, C. -K. Jiang, C. Li, D. Hesk, J. Ge S. Sorota, N. -Y. Shih, F. G. Njoroge, J. A. Kozlowski
Date :  29 Sep 13  (Deposition) - 11 Dec 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna-Dependent Rna Polymerase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Zeng, A. G. Nair, S. B. Rosenblum, H. C. Huang, C. A. Lesburg, Y. Jiang O. Selyutin, T. Y. Chan, F. Bennett, K. X. Chen, S. Venkatraman, M. Sannigrahi, F. Velazquez, J. S. Duca, S. Gavalas, Y. Huang, H. Pu, L. Wang, P. Pinto, B. Vibulbhan, S. Agrawal, E. Ferrari, C. K. Jiang, C. Li, D. Hesk, J. Gesell, S. Sorota, N. Y. Shih, F. G. Njoroge, J. A. Kozlowski
Discovery Of An Irreversible Hcv Ns5B Polymerase Inhibitor.
Bioorg. Med. Chem. Lett. V. 23 6585 2013
PubMed-ID: 24252545  |  Reference-DOI: 10.1016/J.BMCL.2013.10.060

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 2420-2989
    Gene: NS5B
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 420174
    Strain: HC-J4
    Synonym: 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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
12F32Ligand/Ion1-[(2-CHLOROQUINOLIN-3-YL)METHYL]-6-FLUORO-5-METHYL-3-(2-OXO-1,2-DIHYDROPYRIDIN-3-YL)-1H-INDOLE-2-CARBOXYLICACID
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
12F31Ligand/Ion1-[(2-CHLOROQUINOLIN-3-YL)METHYL]-6-FLUORO-5-METHYL-3-(2-OXO-1,2-DIHYDROPYRIDIN-3-YL)-1H-INDOLE-2-CARBOXYLICACID
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12F31Ligand/Ion1-[(2-CHLOROQUINOLIN-3-YL)METHYL]-6-FLUORO-5-METHYL-3-(2-OXO-1,2-DIHYDROPYRIDIN-3-YL)-1H-INDOLE-2-CARBOXYLICACID
2PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:193 , ARG A:200 , ASN A:316 , ASP A:318 , ASP A:319 , CYS A:366 , LEU A:384 , GLY A:410 , ASN A:411 , MET A:414 , TYR A:415 , GLN A:446 , ILE A:447 , TYR A:448 , HOH A:770 , HOH A:847 , HOH A:1060 , HOH A:1121BINDING SITE FOR RESIDUE 2F3 A 601
2AC2SOFTWAREARG A:505 , VAL A:530 , ARG A:531 , THR A:532 , HOH A:799 , HOH A:844 , HOH A:931 , HOH A:978 , HOH A:1133 , HOH A:1141BINDING SITE FOR RESIDUE PO4 A 602
3AC3SOFTWAREPRO A:22 , ARG A:401 , HOH A:907 , HOH A:930 , HOH A:1193 , HOH A:1228 , HOH A:1600 , ARG B:114BINDING SITE FOR RESIDUE PO4 A 603
4AC4SOFTWAREARG A:114 , HOH A:1191 , HOH A:1295 , HOH A:1318 , HOH A:1464 , HOH A:1494 , HOH A:1524 , GLY B:516 , ARG B:517BINDING SITE FOR RESIDUE PO4 A 604
5AC5SOFTWAREPHE B:193 , ARG B:200 , ASN B:316 , ASP B:318 , ASP B:319 , CYS B:366 , LEU B:384 , GLY B:410 , ASN B:411 , TYR B:415 , GLN B:446 , ILE B:447 , TYR B:448 , HOH B:746 , HOH B:841 , HOH B:869 , HOH B:1080 , HOH B:1195BINDING SITE FOR RESIDUE 2F3 B 601

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:303 -A:311

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MZ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4MZ4)

(-) 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:563
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4mz4a_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhh.hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mz4 A   1 SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLGKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAAICGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHSLSRAR 568
                                    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       545       555       565   
                                                                                                                                                                             148|                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                              154                                                                                                                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:560
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4mz4b_ B: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..........................hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh...................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mz4 B   1 SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLGKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAAICGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHSLS 565
                                    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       545       555       565
                                                                                                                                                                             148|                                                                                                                                                                                                                                                                                                                                                                                                                           
                                                                                                                                                                              154
   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 4MZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MZ4)

(-) Gene Ontology  (79, 79)

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_HCVJ4 | O92972: 1nb4 1nb6 1nb7 2f55 2mts 2xhu 2xhv 2xhw 2yoj 3cso 3gnv 3gnw 3gol 3hky 3lkh 3mwv 3mww 3ska 3ske 3skh 3tyq 3tyv 3u4o 3u4r 3uph 3upi 4dru 4eaw 4gmc 4iz0 4j02 4j04 4j06 4j08 4j0a 4jjs 4jju 4jtw 4jty 4jtz 4ju1 4ju2 4ju3 4ju4 4ju6 4ju7 4jvq 4jy0 4jy1 4oow 4ry4 4ry5 4ry6 4ry7 5czb 5nph

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