Structure of PDB 3dle Chain A Binding Site BS01

Receptor Information
>3dle Chain A (length=535) 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
GPENPYNTPVFAIKKTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKK
KSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIE
ELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWT
VNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELEL
AENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGK
YARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWT
EYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLG
KAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYAL
GIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPA
Ligand information
Ligand IDGFA
InChIInChI=1S/C21H16ClNO3/c22-16-11-12-19(18(13-16)21(25)15-7-3-1-4-8-15)26-14-20(24)23-17-9-5-2-6-10-17/h1-13H,14H2,(H,23,24)
InChIKeyDTGVSZSMDOMAEB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Clc2cc(c(OCC(=O)Nc1ccccc1)cc2)C(=O)c3ccccc3
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(=O)c2cc(ccc2OCC(=O)Nc3ccccc3)Cl
CACTVS 3.341Clc1ccc(OCC(=O)Nc2ccccc2)c(c1)C(=O)c3ccccc3
FormulaC21 H16 Cl N O3
Name2-[4-chloro-2-(phenylcarbonyl)phenoxy]-N-phenylacetamide
ChEMBLCHEMBL296939
DrugBankDB07826
ZINC
PDB chain3dle Chain A Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dle Structural basis for the improved drug resistance profile of new generation benzophenone non-nucleoside HIV-1 reverse transcriptase inhibitors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L100 K101 K102 K103 V106 Y188 G190 F227 W229 L234 P236 Y318
Binding residue
(residue number reindexed from 1)		L97 K98 K99 K100 V103 Y185 G187 F224 W226 L231 P233 Y315
Annotation score1
Binding affinityMOAD: ic50=2nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3dle, PDBe:3dle, PDBj:3dle
PDBsum3dle
PubMed18665583
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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