Structure of PDB 8gyb Chain D Binding Site BS01

Receptor Information

>8gyb Chain D (length=247) Species: 2269360 (Alongshan virus)

EVYKGDGYKVWKLEPSLGDPLELGRKTKTEMNAMTHDEFDRMKDKPSKGY
DKLRVLLDLMDRPRLGTTVDLCAGRGGWSELVKDLEGPKGITAVSLWEEW
MADPAIHRINANVKHLRPWQVDTLLFDGGEAFKRDQNLRKEENFNDSLLD
AVDAWMMQPVPPRNFVIKIQVPYTQKAIALLEKWQVKTGKGRLVRLAGDR
LSNTVMYFLSVRLETQIRGRVTTFVRELAERRKDRSLTADPSLQYER

Ligand information

• Ligand ID: SAH
• InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
• InChIKey: ZJUKTBDSGOFHSH-WFMPWKQPSA-N
• SMILES:
  CACTVS 3.341: N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
  CACTVS 3.341: N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
• Formula: C14 H20 N6 O5 S
• Name: S-ADENOSYL-L-HOMOCYSTEINE
• ChEMBL: CHEMBL418052
• DrugBank: DB01752
• ZINC: ZINC000004228232
• PDB chain: 8gyb Chain D Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8gyb Structural and functional analyses of Alongshan virus MTase reveal a low-affinity SAM/SAH-binding enzyme in the Flaviviridae family
• Resolution: 2.101 Å
• Binding residue (original residue number in PDB): S99 C124 G126 G129 W130 S147 L148 N168 V169 D183
• Binding residue (residue number reindexed from 1): S47 C72 G74 G77 W78 S95 L96 N112 V113 D127
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0008168 methyltransferase activity

Biological Process

• GO:0032259 methylation

External links

• PDB: RCSB:8gyb, PDBe:8gyb, PDBj:8gyb
• PDBsum: 8gyb
• PubMed: 37831643
• UniProt: A0A344X2I6