Structure of PDB 8jyj Chain A Binding Site BS03

Receptor Information

>8jyj Chain A (length=144) Species: 587638 (HIV-1 06TG.HT008)

MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQ
KTELQAIYLALQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWKTPVKNV
DLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKV

Ligand information

• Ligand ID: VA9
• InChI: InChI=1S/C26H19NO12/c1-8(28)27-5-4-9-2-3-12(29)10(6-9)15-22(33)19-18(24(35)23(15)34)20(31)11-7-13(30)16(25(36)37)17(26(38)39)14(11)21(19)32/h2-3,6-7,29-30,33-35H,4-5H2,1H3,(H,27,28)(H,36,37)(H,38,39)
• InChIKey: IHLWXZNPOVMUFQ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: CC(=O)NCCc1ccc(O)c(c1)c2c(O)c(O)c3C(=O)c4cc(O)c(C(O)=O)c(C(O)=O)c4C(=O)c3c2O
  OpenEye OEToolkits 2.0.7: CC(=O)NCCc1ccc(c(c1)c2c(c3c(c(c2O)O)C(=O)c4cc(c(c(c4C3=O)C(=O)O)C(=O)O)O)O)O
• Formula: C26 H19 N O12
• Name: 7-[5-(2-acetamidoethyl)-2-oxidanyl-phenyl]-3,5,6,8-tetrakis(oxidanyl)-9,10-bis(oxidanylidene)anthracene-1,2-dicarboxylic acid
• ChEMBL: CHEMBL2037378
• ZINC: ZINC000061389537
• PDB chain: 8jyj Chain A Residue 203

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jyj Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with laccaic acid A
• Resolution: 2.01 Å
• Binding residue (original residue number in PDB): D23 E58 D78 S79 Q80 A128 D139 V149
• Binding residue (residue number reindexed from 1): D18 E53 D73 S74 Q75 A123 D134 V144
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.-
  2.7.7.49: RNA-directed DNA polymerase.
  2.7.7.7: DNA-directed DNA polymerase.
  3.1.-.-
  3.1.13.2: exoribonuclease H.
  3.1.26.13: retroviral ribonuclease H.
  3.4.23.16: HIV-1 retropepsin.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0004523 RNA-DNA hybrid ribonuclease activity

External links

• PDB: RCSB:8jyj, PDBe:8jyj, PDBj:8jyj
• PDBsum: 8jyj
• PubMed: 37874155
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)