Structure of PDB 2qnq Chain A Binding Site BS01

Receptor Information
>2qnq Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDQN3
InChIInChI=1S/C30H29Cl2N3O4S2/c31-25-15-7-9-17-29(25)40(36,37)34(21-23-11-3-1-4-12-23)27-19-33-20-28(27)35(22-24-13-5-2-6-14-24)41(38,39)30-18-10-8-16-26(30)32/h1-18,27-28,33H,19-22H2/t27-,28-/m0/s1
InChIKeyLCDFLCDWPLFFSC-NSOVKSMOSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Clc1ccccc1[S](=O)(=O)N(Cc2ccccc2)[CH]3CNC[CH]3N(Cc4ccccc4)[S](=O)(=O)c5ccccc5Cl
CACTVS 3.341Clc1ccccc1[S](=O)(=O)N(Cc2ccccc2)[C@H]3CNC[C@@H]3N(Cc4ccccc4)[S](=O)(=O)c5ccccc5Cl
OpenEye OEToolkits 1.5.0c1ccc(cc1)CN(C2CNCC2N(Cc3ccccc3)S(=O)(=O)c4ccccc4Cl)S(=O)(=O)c5ccccc5Cl
ACDLabs 10.04O=S(=O)(N(C3C(N(Cc1ccccc1)S(=O)(=O)c2ccccc2Cl)CNC3)Cc4ccccc4)c5ccccc5Cl
OpenEye OEToolkits 1.5.0c1ccc(cc1)CN([C@H]2CNC[C@@H]2N(Cc3ccccc3)S(=O)(=O)c4ccccc4Cl)S(=O)(=O)c5ccccc5Cl
FormulaC30 H29 Cl2 N3 O4 S2
NameN,N'-(3S,4S)-pyrrolidine-3,4-diylbis(N-benzyl-2-chlorobenzenesulfonamide)
ChEMBLCHEMBL1189750
DrugBank
ZINCZINC000095543548
PDB chain2qnq Chain A Residue 2501 [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]
PDB2qnq Structure-Guided Design of C2-Symmetric HIV-1 Protease Inhibitors Based on a Pyrrolidine Scaffold.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D30 G48 I50 V82 I84
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D30 G48 I50 V82 I84
Annotation score1
Binding affinityMOAD: Ki=0.77uM
PDBbind-CN: -logKd/Ki=6.11,Ki=0.77uM
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.
3.4.23.16: HIV-1 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:2qnq, PDBe:2qnq, PDBj:2qnq
PDBsum2qnq
PubMed18348517
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]