Structure of PDB 2yng Chain A Binding Site BS04

Receptor Information
>2yng Chain A (length=560) 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
DKLVSAGIRK
Ligand information
Ligand IDWHU
InChIInChI=1S/C18H11BrCl2FN5O2/c19-12-2-1-9(7-25-17(28)14-16(21)27-18(24)26-14)13(22)15(12)29-11-4-8(6-23)3-10(20)5-11/h1-5H,7H2,(H,25,28)(H3,24,26,27)
InChIKeyIZRLYEGHBQTAFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc(c(c(c1CNC(=O)c2c(nc([nH]2)N)Cl)F)Oc3cc(cc(c3)Cl)C#N)Br
CACTVS 3.385Nc1[nH]c(c(Cl)n1)C(=O)NCc2ccc(Br)c(Oc3cc(Cl)cc(c3)C#N)c2F
ACDLabs 12.01O=C(c1c(Cl)nc(N)n1)NCc3ccc(Br)c(Oc2cc(C#N)cc(Cl)c2)c3F
FormulaC18 H11 Br Cl2 F N5 O2
Name2-azanyl-N-[[4-bromanyl-3-(3-chloranyl-5-cyano-phenoxy)-2-fluoranyl-phenyl]methyl]-4-chloranyl-1H-imidazole-5-carboxamide
ChEMBLCHEMBL2180972
DrugBank
ZINCZINC000095574040
PDB chain2yng Chain A Residue 1563 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yng Rational Design of Potent Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		K102 K103 K104 V106 V108 Y181 Y188 V189 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		K104 K105 K106 V108 V110 Y183 Y190 V191 F229 W231 L236 H237 P238 Y320
Annotation score1
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:2yng, PDBe:2yng, PDBj:2yng
PDBsum2yng
PubMed23137340
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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