Structure of PDB 3lp2 Chain A Binding Site BS01

Receptor Information
>3lp2 Chain A (length=554) Species: 11706 (HIV-1 M:B_HXB2R) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISK
IGPENPYNTPVFAIKTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKN
KSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIE
ELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWT
VNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELEL
AENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGK
YARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWT
EYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLG
KAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYAL
GIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS
AGIR
Ligand information
Ligand IDLP9
InChIInChI=1S/C21H23N3O6/c1-4-23(5-2)13-7-9-14(10-8-13)30-15-11-16-18(25)17(21(27)29-6-3)20(26)24(28)19(16)22-12-15/h7-12,25,28H,4-6H2,1-3H3
InChIKeyZAOGVQGDYHKJCT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCN(CC)c1ccc(cc1)Oc2cc3c(nc2)N(C(=O)C(=C3O)C(=O)OCC)O
CACTVS 3.352CCOC(=O)C1=C(O)c2cc(Oc3ccc(cc3)N(CC)CC)cnc2N(O)C1=O
FormulaC21 H23 N3 O6
Name3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium
ChEMBL
DrugBank
ZINCZINC000103548763
PDB chain3lp2 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3lp2 Structural basis for the inhibition of RNase H activity of HIV-1 reverse transcriptase by RNase H active site-directed inhibitors.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		V108 Y181 Q182 Y188 K223 F227 L228 W229 L234
Binding residue
(residue number reindexed from 1)		V105 Y178 Q179 Y185 K220 F224 L225 W226 L231
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.66,IC50=0.22uM
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:0003964 RNA-directed DNA polymerase activity
GO:0004523 RNA-DNA hybrid ribonuclease activity
Biological Process
GO:0006278 RNA-templated DNA biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3lp2, PDBe:3lp2, PDBj:3lp2
PDBsum3lp2
PubMed20484498
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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