Structure of PDB 3lp1 Chain A Binding Site BS01

Receptor Information
>3lp1 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 IDLP8
InChIInChI=1S/C13H14N2O3/c16-11-9-6-3-7-14-12(9)15(18)13(17)10(11)8-4-1-2-5-8/h3,6-8,16,18H,1-2,4-5H2
InChIKeyQHMJHXXRZXAFLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc2c(nc1)N(C(=O)C(=C2O)C3CCCC3)O
CACTVS 3.352ON1C(=O)C(=C(O)c2cccnc12)C3CCCC3
FormulaC13 H14 N2 O3
Name3-cyclopentyl-1,4-dihydroxy-1,8-naphthyridin-2(1H)-one
ChEMBL
DrugBank
ZINCZINC000103548756
PDB chain3lp1 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3lp1 Structural basis for the inhibition of RNase H activity of HIV-1 reverse transcriptase by RNase H active site-directed inhibitors.
Resolution2.23 Å
Binding residue
(original residue number in PDB)		D443 E478 D498 H539
Binding residue
(residue number reindexed from 1)		D440 E475 D495 H536
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.92,IC50=0.12uM
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:3lp1, PDBe:3lp1, PDBj:3lp1
PDBsum3lp1
PubMed20484498
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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