Structure of PDB 3c6t Chain A Binding Site BS01

Receptor Information
>3c6t Chain A (length=559) Species: 11706 (HIV-1 M:B_HXB2R) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKIS
KIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPA
GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNV
LPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQH
RTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPE
KDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEE
AELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKN
LKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETW
ETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANR
ETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTD
SQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQV
DKLVSAGIR
Ligand information
Ligand IDM14
InChIInChI=1S/C21H14Cl3N3O5S/c22-13-3-12(10-25)4-16(6-13)32-17-7-14(23)5-15(8-17)31-11-21(28)27-20-2-1-18(9-19(20)24)33(26,29)30/h1-9H,11H2,(H,27,28)(H2,26,29,30)
InChIKeyGYBNBRVJAPRVLI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[S](=O)(=O)c1ccc(NC(=O)COc2cc(Cl)cc(Oc3cc(Cl)cc(c3)C#N)c2)c(Cl)c1
OpenEye OEToolkits 1.5.0c1cc(c(cc1S(=O)(=O)N)Cl)NC(=O)COc2cc(cc(c2)Cl)Oc3cc(cc(c3)Cl)C#N
ACDLabs 10.04Clc3cc(ccc3NC(=O)COc2cc(Oc1cc(C#N)cc(Cl)c1)cc(Cl)c2)S(=O)(=O)N
FormulaC21 H14 Cl3 N3 O5 S
Name2-[3-chloro-5-(3-chloro-5-cyanophenoxy)phenoxy]-N-(2-chloro-4-sulfamoylphenyl)acetamide;
N-[4-(aminosulfonyl)-2-chlorophenyl]-2-[3-chloro-5-(3-chloro-5-cyanophenoxy)phenoxy]acetamide
ChEMBLCHEMBL255689
DrugBank
ZINCZINC000029046166
PDB chain3c6t Chain A Residue 561 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3c6t The design and synthesis of diaryl ether second generation HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) with enhanced potency versus key clinical mutations.
Resolution2.7 Å
Binding residue
(original residue number in PDB)
P95 K102 K103 V106 Y181 Y188 F227 W229 P236 Y318
Binding residue
(residue number reindexed from 1)
P97 K104 K105 V108 Y183 Y190 F229 W231 P238 Y320
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.68,IC50=2.11nM
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:3c6t, PDBe:3c6t, PDBj:3c6t
PDBsum3c6t
PubMed18396399
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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