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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-2-(4-FLUOROPHENYL)-N-METHYL-1-BENZOFURAN-3-CARBOXAMIDE
 
Authors :  S. Sheriff
Date :  27 Feb 17  (Deposition) - 10 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ns5B, Polymerase, Hcv, Fingers, Palm, Thumb, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. S. Yeung, B. R. Beno, K. Parcella, J. A. Bender, K. A. Grant-Young, A. Nickel, P. Gunaga, P. Anjanappa, R. O. Bora, K. Selvakumar, K. Rigat Y. K. Wang, M. Liu, J. Lemm, K. Mosure, S. Sheriff, C. Wan, M. Witmer, K. Kish, U. Hanumegowda, X. Zhuo, Y. Z. Shu, D. Parker, R. Haskell, A. Ng Q. Gao, E. Colston, J. Raybon, D. M. Grasela, K. Santone, M. Gao, N. A. Meanwell, M. Sinz, M. G. Soars, J. O. Knipe, S. B. Roberts, J. F. Kadow
Discovery Of A Hepatitis C Virus Ns5B Replicase Palm Site Allosteric Inhibitor (Bms-929075) Advanced To Phase 1 Clinical Studies.
J. Med. Chem. V. 60 4369 2017
PubMed-ID: 28430437  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00328

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS GENOTYPE 1B (ISOLATE CON1)
    Organism Taxid: 333284
    Strain: ISOLATE CON1

 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  (4, 25)

Asymmetric Unit (4, 25)
No.NameCountTypeFull Name
123E2Ligand/Ion(2E)-3-(4-{[(1-{[(13-CYCLOHEXYL-6-OXO-6,7-DIHYDRO-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-YL)CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-ENOIC ACID
28XP2Ligand/Ion5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-2-(4-FLUOROPHENYL)-N-METHYL-1-BENZOFURAN-3-CARBOXAMIDE
3GOL11Ligand/IonGLYCEROL
4SO410Ligand/IonSULFATE ION
Biological Unit 1 (4, 13)
No.NameCountTypeFull Name
123E1Ligand/Ion(2E)-3-(4-{[(1-{[(13-CYCLOHEXYL-6-OXO-6,7-DIHYDRO-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-YL)CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-ENOIC ACID
28XP1Ligand/Ion5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-2-(4-FLUOROPHENYL)-N-METHYL-1-BENZOFURAN-3-CARBOXAMIDE
3GOL7Ligand/IonGLYCEROL
4SO44Ligand/IonSULFATE ION
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
123E1Ligand/Ion(2E)-3-(4-{[(1-{[(13-CYCLOHEXYL-6-OXO-6,7-DIHYDRO-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-YL)CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-ENOIC ACID
28XP1Ligand/Ion5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-2-(4-FLUOROPHENYL)-N-METHYL-1-BENZOFURAN-3-CARBOXAMIDE
3GOL4Ligand/IonGLYCEROL
4SO46Ligand/IonSULFATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:395 , ALA A:396 , HIS A:428 , LEU A:492 , GLY A:493 , VAL A:494 , PRO A:495 , ARG A:498 , VAL A:499 , ARG A:503 , ALA B:400 , 23E B:601 , HOH B:807binding site for residue 23E A 601
02AC2SOFTWAREPRO 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 , LEU A:384 , MET A:414 , TYR A:448 , TYR A:452binding site for residue 8XP A 602
03AC3SOFTWARESER A:84 , VAL A:85 , ARG A:120 , HOH A:717binding site for residue SO4 A 603
04AC4SOFTWAREARG A:48 , LYS A:51 , ARG A:222 , CYS A:223binding site for residue SO4 A 604
05AC5SOFTWAREHIS A:374 , SER A:476 , GLY A:516 , ARG A:517 , HOH A:827binding site for residue SO4 A 605
06AC6SOFTWAREPRO A:496 , LEU A:497 , ARG A:498 , ARG A:570 , HOH A:742binding site for residue SO4 A 606
07AC7SOFTWAREASP A:244 , GOL A:608 , HOH A:733 , ASN B:231binding site for residue GOL A 607
08AC8SOFTWARELYS A:79 , ASP A:244 , GOL A:607 , HOH A:756 , ARG B:65 , ASN B:231 , VAL B:235binding site for residue GOL A 608
09AC9SOFTWARETRP A:208 , ASP A:359 , LEU A:360 , GLU A:361 , TYR A:382 , HOH A:814binding site for residue GOL A 609
10AD1SOFTWAREARG A:65 , ASN A:231 , VAL A:235 , HOH A:829 , LYS B:79 , ASP B:244 , GOL B:609binding site for residue GOL A 610
11AD2SOFTWARESER A:367 , ARG A:386 , THR A:390binding site for residue GOL A 611
12AD3SOFTWARESER A:371 , SER A:478 , PRO A:479 , GLY A:480 , GLU A:481 , HOH A:828binding site for residue GOL A 612
13AD4SOFTWAREALA A:97 , PHE A:162 , ARG A:168 , GLY A:283 , GLY A:557 , ASP A:559binding site for residue GOL A 613
14AD5SOFTWAREALA A:400 , HIS A:428 , 23E A:601 , ALA B:395 , ALA B:396 , HIS B:428 , LEU B:492 , GLY B:493 , VAL B:494 , PRO B:495 , ARG B:498 , VAL B:499 , ARG B:503 , GOL B:611 , HOH B:807binding site for residue 23E B 601
15AD6SOFTWAREPRO B:197 , ARG B:200 , LEU B:204 , LEU B:314 , CYS B:316 , VAL B:321 , ILE B:363 , SER B:365 , CYS B:366 , SER B:368 , LEU B:384 , TYR B:448 , TYR B:452 , HOH B:707binding site for residue 8XP B 602
16AD7SOFTWAREGLY B:516 , ARG B:517binding site for residue SO4 B 603
17AD8SOFTWARESER A:1 , LYS B:379 , ARG B:380binding site for residue SO4 B 604
18AD9SOFTWAREHIS B:475 , SER B:476 , HOH B:816binding site for residue SO4 B 605
19AE1SOFTWAREARG B:48 , LYS B:51 , THR B:221 , ARG B:222 , CYS B:223binding site for residue SO4 B 606
20AE2SOFTWAREPHE B:145 , SER B:367 , ARG B:386 , THR B:390binding site for residue SO4 B 607
21AE3SOFTWARESER B:478 , PRO B:479 , GLY B:480 , GLU B:481 , GOL B:610binding site for residue SO4 B 608
22AE4SOFTWAREASN A:231 , VAL A:235 , GOL A:610 , ASP B:244 , PRO B:247 , HOH B:705binding site for residue GOL B 609
23AE5SOFTWAREASN B:369 , SER B:371 , THR B:385 , SER B:478 , GLU B:481 , ARG B:484 , SO4 B:608binding site for residue GOL B 610
24AE6SOFTWAREALA B:396 , ALA B:400 , 23E B:601binding site for residue GOL B 611
25AE7SOFTWAREGLU A:128 , GLU B:128 , ASP B:129 , THR B:130 , GLU B:131binding site for residue GOL B 612

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5PZN)

(-) 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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.........ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee....eeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.ee..............eee.ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pzn A   1 SMSYTWTGALITPCVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLSRARPRWFM 573
                                    10   ||   42        52        62        72        82        92       102       112       122       132       142   ||  158       168       178       188       198       208       218       228       238       248       258       268       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       568     
                                        14|                                                                                                          146|                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                         37                                                                                                           153                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:540
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeeee..............eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5pzn B   1 SMSYTWTGALITPCYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLS 565
                                    10   ||   43        53        63        73        83        93       103       113       123       133       143     ||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
                                        14|                                                                                                            149|                                                                                                                                                                                                                                                                                                                                                                                                                             
                                         38                                                                                                             152
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  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 5PZN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 74)

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  5pzn
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  POLG_HCVCO | Q9WMX2
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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