Structure of PDB 5vqr Chain A Binding Site BS01

Receptor Information
>5vqr Chain A (length=547) 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]
MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKIS
KIGPENPYNTPVFAIWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKS
VTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKG
SPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEEL
RQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVN
DIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAE
NREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYA
RMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEY
WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKA
GYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGI
IQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLV
Ligand information
Ligand ID9KG
InChIInChI=1S/C28H24N4O5/c1-4-27(34)31(3)22-16-25(18(2)21-15-19(17-29)9-10-20(21)22)37-24-8-6-5-7-23(24)36-14-13-32-12-11-26(33)30-28(32)35/h4-12,15-16H,1,13-14H2,2-3H3,(H,30,33,35)
InChIKeyOFTCTICPJPOVAI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(C(=O)C=C)c1cc(Oc2ccccc2OCCN3C=CC(=O)NC3=O)c(C)c4cc(ccc14)C#N
OpenEye OEToolkits 2.0.6Cc1c2cc(ccc2c(cc1Oc3ccccc3OCCN4C=CC(=O)NC4=O)N(C)C(=O)C=C)C#N
ACDLabs 12.01N1(C=CC(NC1=O)=O)CCOc2c(cccc2)Oc3cc(N(C(\C=C)=O)C)c4c(c3C)cc(cc4)C#N
FormulaC28 H24 N4 O5
NameN-(6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)-N-methylprop-2-enamide
ChEMBLCHEMBL4578515
DrugBank
ZINC
PDB chain5vqr 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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PDB5vqr Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		K101 K102 K103 Y181 Q182 Y188 G190 F227 W229 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		K96 K97 K98 Y176 Q177 Y183 G185 F222 W224 H230 P231 Y313
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.92,IC50=1.2uM
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
View graph for
Biological Process
External links
PDB RCSB:5vqr, PDBe:5vqr, PDBj:5vqr
PDBsum5vqr
PubMed28827354
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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