Structure of PDB 6dtx Chain A Binding Site BS01

Receptor Information
>6dtx Chain A (length=546) Species: 11678 (Human immunodeficiency virus type 1 BH10) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGP
ENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKK
KKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQG
WKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRTKI
EELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSW
TVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELE
LAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTG
KYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWW
TEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKL
GKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYA
LGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQV
Ligand information
Ligand IDH9Y
InChIInChI=1S/C21H14F2N4O4/c22-14-1-2-17(19(8-14)30-6-5-26-4-3-20(28)25-21(26)29)31-18-9-15(23)12-27-11-13(10-24)7-16(18)27/h1-4,7-9,11-12H,5-6H2,(H,25,28,29)
InChIKeyZZRRYEXYIVBDNM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(c(cc1F)OCCN2C=CC(=O)NC2=O)Oc3cc(cn4c3cc(c4)C#N)F
CACTVS 3.385Fc1ccc(Oc2cc(F)cn3cc(cc23)C#N)c(OCCN4C=CC(=O)NC4=O)c1
ACDLabs 12.01N#Cc2cc1c(cc(cn1c2)F)Oc3ccc(cc3OCCN4C(NC(=O)C=C4)=O)F
FormulaC21 H14 F2 N4 O4
Name8-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-6-fluoroindolizine-2-carbonitrile
ChEMBLCHEMBL3342978
DrugBank
ZINCZINC000210929423
PDB chain6dtx Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6dtx Molecular and cellular studies evaluating a potent 2-cyanoindolizine catechol diether NNRTI targeting wildtype and Y181C mutant HIV-1 reverse transcriptase.
Resolution3.327 Å
Binding residue
(original residue number in PDB)		L100 K102 K103 V106 V108 Y181 Y188 F227 W229 P236 Y318
Binding residue
(residue number reindexed from 1)		L98 K100 K101 V104 V106 Y179 Y186 F225 W227 P234 Y316
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.35,IC50=4.5nM
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:6dtx, PDBe:6dtx, PDBj:6dtx
PDBsum6dtx
PubMed31281023
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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