Structure of PDB 6upj Chain A Binding Site BS01

Receptor Information
>6upj Chain A (length=99) Species: 11709 (Human immunodeficiency virus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGI
GGFINTLEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL
Ligand information
Ligand IDNIU
InChIInChI=1S/C19H22O3/c1-2-14(13-9-5-3-6-10-13)17-18(20)15-11-7-4-8-12-16(15)22-19(17)21/h3,5-6,9-10,14,20H,2,4,7-8,11-12H2,1H3/t14-/m0/s1
InChIKeyYKJXQZGJGDTEOC-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCC(c1ccccc1)C2=C(C3=C(CCCCC3)OC2=O)O
CACTVS 3.341CC[CH](c1ccccc1)C2=C(O)C3=C(CCCCC3)OC2=O
ACDLabs 10.04O=C1OC3=C(C(O)=C1C(c2ccccc2)CC)CCCCC3
OpenEye OEToolkits 1.5.0CC[C@@H](c1ccccc1)C2=C(C3=C(CCCCC3)OC2=O)O
CACTVS 3.341CC[C@@H](c1ccccc1)C2=C(O)C3=C(CCCCC3)OC2=O
FormulaC19 H22 O3
Name6,7,8,9-TETRAHYDRO-4-HYDROXY-3-(1-PHENYLPROPYL)CYCLOHEPTA[B]PYRAN-2-ONE
ChEMBL
DrugBankDB08274
ZINCZINC000013741430
PDB chain6upj Chain A Residue 100 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6upj Use of medium-sized cycloalkyl rings to enhance secondary binding: discovery of a new class of human immunodeficiency virus (HIV) protease inhibitors.
Resolution2.34 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 I50
Binding residue
(residue number reindexed from 1)		D25 G27 A28 I50
Annotation score1
Binding affinityMOAD: Ki=480nM
PDBbind-CN: -logKd/Ki=6.32,Ki=480nM
Enzymatic activity
Catalytic site (original residue number in PDB) D25 T26 G27
Catalytic site (residue number reindexed from 1) D25 T26 G27
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.
3.4.23.47: HIV-2 retropepsin.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6upj, PDBe:6upj, PDBj:6upj
PDBsum6upj
PubMed7783120
UniProtP04584|POL_HV2RO Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]