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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 4-FLUORO-2-(4-FLUOROPHENYL)-N-METHYL-5-(2-METHYL-5-{[1-(PYRIMIDIN-2-YL)CYCLOPROPYL]CARBAMOYL}PHENYL)-1-BENZOFURAN-3-CARBOXAMIDE (BMS-929075)
 
Authors :  S. Sheriff
Date :  27 Feb 17  (Deposition) - 10 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
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, 16)

Asymmetric Unit (4, 16)
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
28XJ2Ligand/Ion4-FLUORO-2-(4-FLUOROPHENYL)-N-METHYL-5-(2-METHYL-5-{[1-(PYRIMIDIN-2-YL)CYCLOPROPYL]CARBAMOYL}PHENYL)-1-BENZOFURAN-3-CARBOXAMIDE
3GOL4Ligand/IonGLYCEROL
4SO48Ligand/IonSULFATE ION
Biological Unit 1 (4, 9)
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
28XJ1Ligand/Ion4-FLUORO-2-(4-FLUOROPHENYL)-N-METHYL-5-(2-METHYL-5-{[1-(PYRIMIDIN-2-YL)CYCLOPROPYL]CARBAMOYL}PHENYL)-1-BENZOFURAN-3-CARBOXAMIDE
3GOL3Ligand/IonGLYCEROL
4SO44Ligand/IonSULFATE ION
Biological Unit 2 (4, 7)
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
28XJ1Ligand/Ion4-FLUORO-2-(4-FLUOROPHENYL)-N-METHYL-5-(2-METHYL-5-{[1-(PYRIMIDIN-2-YL)CYCLOPROPYL]CARBAMOYL}PHENYL)-1-BENZOFURAN-3-CARBOXAMIDE
3GOL1Ligand/IonGLYCEROL
4SO44Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:392 , ALA A:395 , ALA A:396 , HIS A:428 , LEU A:492 , GLY A:493 , VAL A:494 , PRO A:495 , PRO A:496 , ARG A:498 , VAL A:499 , TRP A:500 , ARG A:503 , 23E B:601binding site for residue 23E A 601
02AC2SOFTWARETYR A:195 , PRO A:197 , ARG A:200 , LEU A:204 , LEU A:314 , CYS A:316 , ILE A:363 , SER A:365 , CYS A:366 , SER A:368 , MET A:414 , ILE A:447 , TYR A:448 , TYR A:452 , LEU A:466 , TRP A:550binding site for residue 8XJ A 602
03AC3SOFTWAREHIS A:374 , SER A:476 , GLY A:516 , ARG A:517binding site for residue SO4 A 603
04AC4SOFTWAREPRO A:496 , LEU A:497 , ARG A:498 , ARG A:570 , HOH A:708binding site for residue SO4 A 604
05AC5SOFTWARESER A:371 , SER A:478 , LYS A:523binding site for residue SO4 A 605
06AC6SOFTWAREPHE A:145 , SER A:367 , ARG A:386 , THR A:390binding site for residue SO4 A 606
07AC7SOFTWAREASP A:244 , LEU A:245 , ALA A:246binding site for residue GOL A 607
08AC8SOFTWARETRP A:208 , ASP A:359 , LEU A:360 , GLU A:361 , TYR A:382binding site for residue GOL A 608
09AC9SOFTWARECYS A:213 , HIS A:502 , ARG A:505 , ARG A:531binding site for residue GOL A 609
10AD1SOFTWAREALA A:400 , 23E A:601 , LEU B:392 , ALA B:393 , ALA B:395 , ALA B:396 , ILE B:424 , HIS B:428 , LEU B:492 , GLY B:493 , VAL B:494 , PRO B:495 , PRO B:496 , ARG B:498 , VAL B:499 , ARG B:503binding site for residue 23E B 601
11AD2SOFTWARETYR B:195 , SER B:196 , PRO 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 , MET B:414 , TYR B:448binding site for residue 8XJ B 602
12AD3SOFTWAREGLY B:516 , ARG B:517binding site for residue SO4 B 603
13AD4SOFTWARESER A:1 , LYS B:379 , ARG B:380binding site for residue SO4 B 604
14AD5SOFTWAREHIS B:475 , SER B:476binding site for residue SO4 B 605
15AD6SOFTWARESER B:367 , ARG B:386 , THR B:390binding site for residue SO4 B 606
16AD7SOFTWAREASN B:369 , SER B:371 , GLU B:481 , ARG B:484binding site for residue GOL B 607

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5PZP)

(-) 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..............hhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhhhh......eeeeee...........eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeee....eeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhheehhhhhhh.......ee..ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pzp A   1 SMSYTWTGALITPCYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLSRARPRWFM 573
                                    10   ||   43        53        63        73        83        93       103       113       123       133       143     ||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|                                                                                                            149|                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                         38                                                                                                             155                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:535
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..............hhhhhhhhh........hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeeee...........eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pzp B   1 SMSYTWTGALITPCYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHS 563
                                    10   ||   43        53        63        73        83        93       103       113       123       133       143     ||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     
                                        14|                                                                                                            149|                                                                                                                                                                                                                                                                                                                                                                                                                        
                                         38                                                                                                             155
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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 5PZP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 74)

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  5pzp
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  POLG_HCVCO | Q9WMX2
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 Related Entries

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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 5pzn 5pzo 5trh 5tri 5trj 5trk 5twn

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