Structure of PDB 3di6 Chain A Binding Site BS01

Receptor Information
>3di6 Chain A (length=551) Species: 11706 (HIV-1 M:B_HXB2R) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKK
SVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWK
GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEE
LRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTV
NDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELA
ENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKY
ARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTE
YWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGK
AGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALG
IIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA
G
Ligand information
Ligand IDPDZ
InChIInChI=1S/C17H12ClFN2O2/c18-14-8-6-11(10-12-7-9-15(22)21-20-12)16(19)17(14)23-13-4-2-1-3-5-13/h1-9H,10H2,(H,21,22)
InChIKeyNOVPOXGMADEKPP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1C=CC(=NN1)Cc3ccc(Cl)c(Oc2ccccc2)c3F
CACTVS 3.341Fc1c(CC2=NNC(=O)C=C2)ccc(Cl)c1Oc3ccccc3
OpenEye OEToolkits 1.5.0c1ccc(cc1)Oc2c(ccc(c2F)CC3=NNC(=O)C=C3)Cl
FormulaC17 H12 Cl F N2 O2
Name6-(4-chloro-2-fluoro-3-phenoxybenzyl)pyridazin-3(2H)-one
ChEMBLCHEMBL479032
DrugBankDB08379
ZINCZINC000040404526
PDB chain3di6 Chain A Residue 562 [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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PDB3di6 Discovery and optimization of pyridazinone non-nucleoside inhibitors of HIV-1 reverse transcriptase.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		L100 K103 V106 Y181 Y188 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L96 K99 V102 Y177 Y184 W225 L230 H231 P232 Y314
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.00,IC50=0.1uM
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
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Biological Process
External links
PDB RCSB:3di6, PDBe:3di6, PDBj:3di6
PDBsum3di6
PubMed18632268
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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