Structure of PDB 3gyn Chain A Binding Site BS01

Receptor Information

>3gyn Chain A (length=557) Species: 11105 (Hepatitis C virus (isolate BK))

SMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGLRQK
KVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSK
FGYGAKDVRNLSSKAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQRK
PARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLV
NTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKS
LTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRA
AKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQ
PEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPV
NSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIE
PLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRAR
SVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIPAASQLDLSGWFVAGY
SGGDIYH

Ligand information

• Ligand ID: B42
• InChI: InChI=1S/C24H34N4O6S2/c1-15(2)11-12-24(3)14-28(17-7-5-6-8-17)23(30)20(21(24)29)22-25-18-10-9-16(26-35(4,31)32)13-19(18)36(33,34)27-22/h9-10,13,15,17,26,29H,5-8,11-12,14H2,1-4H3,(H,25,27)/t24-/m1/s1
• InChIKey: TXEOLWVIZKSKML-XMMPIXPASA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)CCC1(CN(C(=O)C(=C1O)C2=NS(=O)(=O)c3cc(ccc3N2)NS(=O)(=O)C)C4CCCC4)C
  CACTVS 3.341: CC(C)CC[C]1(C)CN(C2CCCC2)C(=O)C(=C1O)C3=N[S](=O)(=O)c4cc(N[S](C)(=O)=O)ccc4N3
  OpenEye OEToolkits 1.5.0: CC(C)CC[C@@]1(CN(C(=O)C(=C1O)C2=NS(=O)(=O)c3cc(ccc3N2)NS(=O)(=O)C)C4CCCC4)C
  ACDLabs 10.04: O=S(=O)(Nc1ccc2c(c1)S(=O)(=O)N=C(N2)C3=C(O)C(C)(CCC(C)C)CN(C3=O)C4CCCC4)C
  CACTVS 3.341: CC(C)CC[C@]1(C)CN(C2CCCC2)C(=O)C(=C1O)C3=N[S](=O)(=O)c4cc(N[S](C)(=O)=O)ccc4N3
• Formula: C24 H34 N4 O6 S2
• Name: N-{3-[(5R)-1-cyclopentyl-4-hydroxy-5-methyl-5-(3-methylbutyl)-2-oxo-1,2,5,6-tetrahydropyridin-3-yl]-1,1-dioxido-4H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide;
  N-[3-[(5R)-1-cyclopentyl-4-hydroxy-5-methyl-5-(3-methylbutyl)-2-oxo-6H-pyridin-3-yl]-1,1-dioxo-4H-benzo[e][1,2,4]thiadiazin-7-yl]methanesulfonamide
• ChEMBL: CHEMBL566079
• ZINC: ZINC000100095145
• PDB chain: 3gyn Chain A Residue 579

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gyn 5,5'- and 6,6'-dialkyl-5,6-dihydro-1H-pyridin-2-ones as potent inhibitors of HCV NS5B polymerase.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): F193 N291 D318 C366 L384 G410 N411 M414 Y415 Y448 S556
• Binding residue (residue number reindexed from 1): F188 N286 D313 C361 L379 G405 N406 M409 Y410 Y443 S551
• Annotation score: 1
• Binding affinity: MOAD: ic50=0.047uM
  PDBbind-CN: -logKd/Ki=7.21,IC50=0.061uM

Enzymatic activity

• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.
  3.4.21.98: hepacivirin.
  3.4.22.-
  3.6.1.15: nucleoside-triphosphate phosphatase.
  3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003968 RNA-dependent RNA polymerase activity

Biological Process

• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:3gyn, PDBe:3gyn, PDBj:3gyn
• PDBsum: 3gyn
• PubMed: 19796938
• UniProt: P26663|POLG_HCVBK Genome polyprotein