Structure of PDB 2ynf Chain A Binding Site BS04

Receptor Information
>2ynf Chain A (length=557) 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
KIGPENPYNTPVFAIKSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLK
KKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQ
GWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLLVGSDLEIGQHRTK
IEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDS
WTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAEL
ELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKT
GKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETW
WTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETK
LGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQY
ALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKL
VSAGIRK
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 chain2ynf Chain A Residue 1563 [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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PDB2ynf Rational Design of Potent Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase.
Resolution2.36 Å
Binding residue
(original residue number in PDB)		L100 K102 K103 K104 V106 V108 Y181 L188 V189 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L99 K101 K102 K103 V105 V107 Y180 L187 V188 F226 W228 L233 H234 P235 Y317
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ynf, PDBe:2ynf, PDBj:2ynf
PDBsum2ynf
PubMed23137340
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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