Structure of PDB 8jyh Chain A Binding Site BS03

Receptor Information
>8jyh Chain A (length=144) Species: 587638 (HIV-1 06TG.HT008) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQ
KTELQAIYLALQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWKTPVKNV
DLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKV
Ligand information
Ligand IDV96
InChIInChI=1S/C25H17NO13/c26-9(23(34)35)4-6-1-2-10(27)7(3-6)13-20(31)17-16(22(33)21(13)32)18(29)8-5-11(28)14(24(36)37)15(25(38)39)12(8)19(17)30/h1-3,5,9,27-28,31-33H,4,26H2,(H,34,35)(H,36,37)(H,38,39)/t9-/m0/s1
InChIKeyVRXULZFQCGXCRV-VIFPVBQESA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[C@@H](Cc1ccc(O)c(c1)c2c(O)c(O)c3C(=O)c4cc(O)c(C(O)=O)c(C(O)=O)c4C(=O)c3c2O)C(O)=O
CACTVS 3.385N[CH](Cc1ccc(O)c(c1)c2c(O)c(O)c3C(=O)c4cc(O)c(C(O)=O)c(C(O)=O)c4C(=O)c3c2O)C(O)=O
OpenEye OEToolkits 2.0.7c1cc(c(cc1C[C@@H](C(=O)O)N)c2c(c3c(c(c2O)O)C(=O)c4cc(c(c(c4C3=O)C(=O)O)C(=O)O)O)O)O
OpenEye OEToolkits 2.0.7c1cc(c(cc1CC(C(=O)O)N)c2c(c3c(c(c2O)O)C(=O)c4cc(c(c(c4C3=O)C(=O)O)C(=O)O)O)O)O
FormulaC25 H17 N O13
Name7-[5-[(2~{S})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]-2-oxidanyl-phenyl]-3,5,6,8-tetrakis(oxidanyl)-9,10-bis(oxidanylidene)anthracene-1,2-dicarboxylic acid
ChEMBL
DrugBank
ZINCZINC000085994782
PDB chain8jyh Chain A Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8jyh Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with laccaic acid C
Resolution2.21 Å
Binding residue
(original residue number in PDB)		D23 E58 D78 S79 Q80 Y81 A128 H129 D139
Binding residue
(residue number reindexed from 1)		D18 E53 D73 S74 Q75 Y76 A123 H124 D134
Annotation score1
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

View graph for
Molecular Function
External links
PDB RCSB:8jyh, PDBe:8jyh, PDBj:8jyh
PDBsum8jyh
PubMed37874155
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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