Structure of PDB 5vqz Chain A Binding Site BS01

Receptor Information
>5vqz 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
KIGPENPYNTPVFAIWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKNKS
VTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKG
SPAIFQSSMTKILEPFAAQNPDIVICQYMDDLYVGSDLEIGQHRTKIEEL
RQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVN
DIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAE
NREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYA
RMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEY
WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKA
GYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGI
IQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLV
Ligand information
Ligand ID9HY
InChIInChI=1S/C27H24N4O5/c1-17-21-14-19(16-28)8-9-20(21)22(30(3)18(2)32)15-25(17)36-24-7-5-4-6-23(24)35-13-12-31-11-10-26(33)29-27(31)34/h4-11,14-15H,12-13H2,1-3H3,(H,29,33,34)
InChIKeyBUPXJFBLNQOLSS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c2cc(ccc2c(cc1Oc3ccccc3OCCN4C=CC(=O)NC4=O)N(C)C(=O)C)C#N
CACTVS 3.385CN(C(C)=O)c1cc(Oc2ccccc2OCCN3C=CC(=O)NC3=O)c(C)c4cc(ccc14)C#N
ACDLabs 12.01CC(=O)N(C)c1c4ccc(C#N)cc4c(C)c(c1)Oc2c(cccc2)OCCN3C(NC(C=C3)=O)=O
FormulaC27 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-methylacetamide
ChEMBL
DrugBank
ZINC
PDB chain5vqz 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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PDB5vqz Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography.
Resolution2.23 Å
Binding residue
(original residue number in PDB)
K101 K102 N103 C181 Y188 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)
K96 K97 N98 C176 Y183 F222 W224 L229 H230 P231 Y313
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.39,IC50=0.41uM
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:5vqz, PDBe:5vqz, PDBj:5vqz
PDBsum5vqz
PubMed28827354
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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