Structure of PDB 2i5j Chain A Binding Site BS04

Receptor Information
>2i5j Chain A (length=552) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK
LV
Ligand information
Ligand IDK05
InChIInChI=1S/C19H16N2O4/c1-25-18-9-7-12-4-2-3-5-14(12)15(18)11-20-21-19(24)13-6-8-16(22)17(23)10-13/h2-11,22-23H,1H3,(H,21,24)/b20-11+
InChIKeyTVOPERZEGKBKAY-RGVLZGJSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1ccc2ccccc2c1C=NNC(=O)c3ccc(O)c(O)c3
CACTVS 3.341COc1ccc2ccccc2c1/C=N/NC(=O)c3ccc(O)c(O)c3
OpenEye OEToolkits 1.5.0COc1ccc2ccccc2c1C=NNC(=O)c3ccc(c(c3)O)O
OpenEye OEToolkits 1.5.0COc1ccc2ccccc2c1\C=N\NC(=O)c3ccc(c(c3)O)O
ACDLabs 10.04O=C(c1cc(O)c(O)cc1)N/N=C/c3c2ccccc2ccc3OC
FormulaC19 H16 N2 O4
Name(E)-3,4-DIHYDROXY-N'-[(2-METHOXYNAPHTHALEN-1-YL)METHYLENE]BENZOHYDRAZIDE
ChEMBLCHEMBL1233795
DrugBankDB08034
ZINCZINC000000074303
PDB chain2i5j Chain A Residue 4001 [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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PDB2i5j HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		V108 D186 L187 Y188 K223 L228 W229
Binding residue
(residue number reindexed from 1)		V108 D186 L187 Y188 K223 L228 W229
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.30,IC50=0.5uM
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:2i5j, PDBe:2i5j, PDBj:2i5j
PDBsum2i5j
PubMed17184135
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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