Structure of PDB 6x4b Chain A Binding Site BS01

Receptor Information
>6x4b Chain A (length=549) 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]
ISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIG
PENPYNTPVFAIKKKTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKK
KSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNGIRYQYNVLPQGWKGS
PAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELR
QHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVND
IQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAEN
REILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYAR
MRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYW
QATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAG
YVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGII
QAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG
Ligand information
Ligand IDUMY
InChIInChI=1S/C24H18FN3O4/c1-15-18-12-16(14-26)6-7-17(18)19(25)13-22(15)32-21-5-3-2-4-20(21)31-11-10-28-9-8-23(29)27-24(28)30/h2-9,12-13H,10-11H2,1H3,(H,27,29,30)
InChIKeyOIPOKGOOHCBAPR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c2cc(ccc2c(cc1Oc3ccccc3OCCN4C=CC(=O)NC4=O)F)C#N
CACTVS 3.385Cc1c(Oc2ccccc2OCCN3C=CC(=O)NC3=O)cc(F)c4ccc(cc14)C#N
ACDLabs 12.01c2(c1c(cc(cc1)C#N)c(C)c(c2)Oc4ccccc4OCCN3C=CC(=O)NC3=O)F
FormulaC24 H18 F N3 O4
Name7-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-5-fluoro-8-methylnaphthalene-2-carbonitrile
ChEMBLCHEMBL3967150
DrugBank
ZINC
PDB chain6x4b Chain A Residue 601 [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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PDB6x4b Structural investigation of 2-naphthyl phenyl ether inhibitors bound to WT and Y181C reverse transcriptase highlights key features of the NNRTI binding site.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L100 K101 K102 K103 V106 V108 V179 Y181 Y188 V189 G190 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L97 K98 K99 K100 V103 V105 V173 Y175 Y182 V183 G184 W223 L228 H229 P230 Y312
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
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Biological Process
External links
PDB RCSB:6x4b, PDBe:6x4b, PDBj:6x4b
PDBsum6x4b
PubMed32643196
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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