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(-) Description

Title :  HCV NS5B IN COMPLEX WITH LIGAND IDX17119-5
 
Authors :  C. Pierra, C. Dousson, M. Augustin
Date :  31 Jul 15  (Deposition) - 15 Jun 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hcv Polymerase, Idenix, Inhibitor, Proteros Biostructures Gmbh, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Pierra Rouviere, A. Amador, E. Badaroux, T. Convard, D. Da Costa, D. Dukhan, L. Griffe, J. F. Griffon, M. Lacolla, F. Leroy, M. Liuzzi, A. G. Loi, J. Mccarville, V. Mascia, J. Milhau, L. Onidi, J. L. Paparin, R. Rahali, E. Sais, M. Seifer, D. Surleraux, D. Standring, C. Dousson
Synthesis Of Potent And Broad Genotypically Active Ns5B Hcv Non-Nucleoside Inhibitors Binding To The Thumb Domain Allosteric Site 2 Of The Viral Polymerase.
Bioorg. Med. Chem. Lett. V. 26 4536 2016
PubMed-ID: 27520942  |  Reference-DOI: 10.1016/J.BMCL.2016.01.042

(-) Compounds

Molecule 1 - NS5B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS SUBTYPE 1B
    Organism Taxid: 31647

 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  (5, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
155W2Ligand/Ion1-[4-(7-AMINO-5-METHYLPYRAZOLO[1,5-A]PYRIMIDIN-2-YL)PHENYL]-3-{[(R)-(2,4-DIMETHYLPHENYL)(METHOXY)PHOSPHORYL]AMINO}-1H-PYRAZOLE-4-CARBOXYLIC ACID
2GOL7Ligand/IonGLYCEROL
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
5SO413Ligand/IonSULFATE ION
Biological Unit 1 (5, 18)
No.NameCountTypeFull Name
155W1Ligand/Ion1-[4-(7-AMINO-5-METHYLPYRAZOLO[1,5-A]PYRIMIDIN-2-YL)PHENYL]-3-{[(R)-(2,4-DIMETHYLPHENYL)(METHOXY)PHOSPHORYL]AMINO}-1H-PYRAZOLE-4-CARBOXYLIC ACID
2GOL2Ligand/IonGLYCEROL
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5SO410Ligand/IonSULFATE ION
Biological Unit 2 (4, 11)
No.NameCountTypeFull Name
155W1Ligand/Ion1-[4-(7-AMINO-5-METHYLPYRAZOLO[1,5-A]PYRIMIDIN-2-YL)PHENYL]-3-{[(R)-(2,4-DIMETHYLPHENYL)(METHOXY)PHOSPHORYL]AMINO}-1H-PYRAZOLE-4-CARBOXYLIC ACID
2GOL5Ligand/IonGLYCEROL
3MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5SO43Ligand/IonSULFATE ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:422 , MET A:423 , LEU A:474 , HIS A:475 , SER A:476 , TYR A:477 , ILE A:482 , LEU A:489 , ARG A:490 , VAL A:494 , PRO A:495 , PRO A:496 , LEU A:497 , ARG A:501 , TRP A:528 , HOH A:739 , HOH A:760binding site for residue 55W A 601
02AC2SOFTWAREALA A:97 , LYS A:98 , HOH A:822binding site for residue GOL A 602
03AC3SOFTWARETHR A:499 , ARG A:503 , HOH A:812binding site for residue GOL A 603
04AC4SOFTWARELEU A:497 , ARG A:498 , ARG A:501 , GLU B:202 , VAL B:205 , ASN B:206 , TYR B:382binding site for residue MES A 604
05AC5SOFTWARELEU A:83 , ARG A:120 , HOH A:708binding site for residue PEG A 605
06AC6SOFTWAREGLU A:248 , GLN A:251 , HOH A:862 , THR B:130 , GLU B:131 , ARG B:254 , GLU B:258binding site for residue PEG A 606
07AC7SOFTWARELEU A:469 , SER A:470binding site for residue PEG A 607
08AC8SOFTWARESER A:96 , ALA A:97 , GLY A:283 , GLY A:557 , HOH A:724binding site for residue PEG A 608
09AC9SOFTWAREGLU A:440 , GLY A:516 , ARG A:517binding site for residue SO4 A 609
10AD1SOFTWAREARG A:498 , ARG A:505 , HOH A:953binding site for residue SO4 A 610
11AD2SOFTWARESER A:112 , SER A:113 , HOH A:911binding site for residue SO4 A 611
12AD3SOFTWAREARG A:48 , LYS A:51 , THR A:221 , CYS A:223 , HOH A:832 , HOH A:933binding site for residue SO4 A 612
13AD4SOFTWAREARG A:114 , HOH A:749 , PRO B:22 , ILE B:23 , ASN B:24 , ARG B:401binding site for residue SO4 A 613
14AD5SOFTWAREHIS A:502 , ARG A:505 , HOH A:854binding site for residue SO4 A 614
15AD6SOFTWAREARG A:498 , HOH A:705 , HOH A:713 , HOH A:740 , HOH A:937 , HOH A:988 , GLN B:199binding site for residue SO4 A 615
16AD7SOFTWARETHR A:287 , ASN A:291 , GLY A:317 , ASP A:318 , HOH A:774binding site for residue SO4 A 616
17AD8SOFTWAREARG A:32 , HIS A:33 , HIS A:34 , ASN A:35binding site for residue SO4 A 617
18AD9SOFTWARELYS A:79 , ASP A:244 , HOH A:1003 , LEU B:60 , LEU B:68 , HOH B:764binding site for residue SO4 A 618
19AE1SOFTWARELEU B:419 , ARG B:422 , MET B:423 , LEU B:474 , HIS B:475 , SER B:476 , TYR B:477 , ILE B:482 , LEU B:489 , ARG B:490 , VAL B:494 , PRO B:495 , PRO B:496 , LEU B:497 , TRP B:528 , SO4 B:611 , HOH B:816 , HOH B:1003binding site for residue 55W B 601
20AE2SOFTWAREARG B:380 , TYR B:382 , HOH B:970binding site for residue GOL B 602
21AE3SOFTWARESER B:96 , ALA B:97 , PHE B:162 , ARG B:168binding site for residue GOL B 603
22AE4SOFTWAREARG B:43 , HOH B:940binding site for residue GOL B 604
23AE5SOFTWAREGLU B:143 , GLN B:446 , SER B:556 , HOH B:864binding site for residue GOL B 605
24AE6SOFTWAREHIS B:502 , ARG B:505binding site for residue GOL B 606
25AE7SOFTWAREGLU A:124 , ASP A:125 , GLU A:128 , HOH A:827 , ARG B:32 , PRO B:496 , THR B:499 , HOH B:969binding site for residue PEG B 607
26AE8SOFTWAREGLU B:464 , LEU B:469 , SER B:470 , HOH B:730binding site for residue PEG B 608
27AE9SOFTWARETHR B:287 , SER B:288 , ASN B:291 , GLY B:317 , ASP B:318 , SER B:556 , HOH B:955binding site for residue SO4 B 609
28AF1SOFTWAREGLY B:516 , ARG B:517binding site for residue SO4 B 610
29AF2SOFTWAREPRO B:496 , LEU B:497 , ARG B:498 , 55W B:601 , HOH B:1011binding site for residue SO4 B 611

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CZB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CZB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CZB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CZB)

(-) Exons   (0, 0)

(no "Exon" information available for 5CZB)

(-) 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:555
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...................hhhhh..hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee...eee.........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............................ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5czb A   0 SSMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPDLSGWFVAGYSGGDIYH 562
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149|      162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       547       557     
                                                                                                                                                                               149|                                                                                                                                                                                                                                                                                                                                                                                                540|                
                                                                                                                                                                                153                                                                                                                                                                                                                                                                                                                                                                                                 546                


Chain B from PDB  Type:PROTEIN  Length:557
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh............................ee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5czb B   1 SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASDLSGWFVAGYSGGDIYH 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       543|      555       
                                                                                                                                                                              149|                                                                                                                                                                                                                                                                                                                                                                                                   543|                
                                                                                                                                                                               153                                                                                                                                                                                                                                                                                                                                                                                                    546
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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 5CZB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CZB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CZB)

(-) Gene Ontology  (79, 79)

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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 4mz4 4oow 4ry4 4ry5 4ry6 4ry7 5nph

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