Structure of PDB 3dlg Chain A Binding Site BS01

Receptor Information
>3dlg Chain A (length=532) 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
GPENPYNTPVFAIKKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKS
VTVLDVGDAYFSVPLDEDFRKYTAFTIPSIETPGIRYQYNVLPQGWKGSP
AIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQ
HLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDI
QKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENR
EILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARM
RGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQ
ATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGY
VTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQ
AQPDQSESELVNQIIEQLIKKEKVYLAWVPAH
Ligand information
Ligand IDGWE
InChIInChI=1S/C23H19ClF4N2O5S/c1-12-6-17(36(29,33)34)3-4-19(12)30-21(31)11-35-20-5-2-15(24)10-18(20)22(32)13-7-14(23(26,27)28)9-16(25)8-13/h2-10,33-34H,11,29H2,1H3,(H,30,31)
InChIKeyRXLXGVALXIAUEE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1cc(ccc1NC(=O)COc2ccc(cc2C(=O)c3cc(cc(c3)F)C(F)(F)F)Cl)S(N)(O)O
CACTVS 3.341Cc1cc(ccc1NC(=O)COc2ccc(Cl)cc2C(=O)c3cc(F)cc(c3)C(F)(F)F)[S](N)(O)O
ACDLabs 10.04Clc2cc(c(OCC(=O)Nc1ccc(cc1C)S(O)(O)N)cc2)C(=O)c3cc(F)cc(c3)C(F)(F)F
FormulaC23 H19 Cl F4 N2 O5 S
NameN-{4-[amino(dihydroxy)-lambda~4~-sulfanyl]-2-methylphenyl}-2-(4-chloro-2-{[3-fluoro-5-(trifluoromethyl)phenyl]carbonyl}phenoxy)acetamide
ChEMBL
DrugBank
ZINCZINC000103543969
PDB chain3dlg Chain A Residue 999 [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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PDB3dlg Structural basis for the improved drug resistance profile of new generation benzophenone non-nucleoside HIV-1 reverse transcriptase inhibitors.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		L100 K101 K102 K103 K104 S105 V106 V179 Y181 Y188 G190 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L95 K96 K97 K98 K99 S100 V101 V172 Y174 Y181 G183 F220 W222 L227 H228 P229 Y311
Annotation score1
Binding affinityMOAD: ic50=1.2nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dlg, PDBe:3dlg, PDBj:3dlg
PDBsum3dlg
PubMed18665583
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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