Structure of PDB 2qd6 Chain B Binding Site BS01

Receptor Information
>2qd6 Chain B (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]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGV
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand ID065
InChIInChI=1S/C28H36N2O9S/c1-18(2)14-30(40(33,34)20-8-9-24-25(13-20)38-17-37-24)15-23(31)22(12-19-6-4-3-5-7-19)29-28(32)39-26-16-36-27-21(26)10-11-35-27/h3-9,13,18,21-23,26-27,31H,10-12,14-17H2,1-2H3,(H,29,32)/t21-,22-,23+,26-,27+/m0/s1
InChIKeyHNEIRZJZTYYDES-VPZBFSRCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2COC3C2CCO3)O)S(=O)(=O)c4ccc5c(c4)OCO5
OpenEye OEToolkits 1.5.0CC(C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)c4ccc5c(c4)OCO5
CACTVS 3.341CC(C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)O[CH]2CO[CH]3OCC[CH]23)[S](=O)(=O)c4ccc5OCOc5c4
ACDLabs 10.04O=S(=O)(c2ccc1OCOc1c2)N(CC(C)C)CC(O)C(NC(=O)OC3COC4OCCC34)Cc5ccccc5
CACTVS 3.341CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@H]3OCC[C@@H]23)[S](=O)(=O)c4ccc5OCOc5c4
FormulaC28 H36 N2 O9 S
Name(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(2S,3R)-3-HYDROXY-4-(N-ISOBUTYLBENZO[D][1,3]DIOXOLE-5-SULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE;
RL-98065;
[(1R,5S,6R)-2,8-DIOXABICYCLO[3.3.0]OCT-6-YL]N-[(2S,3R)-4-[(3,4-METHYLENEDIOXYPHENYL)SULFONYL-(2-METHYLPROPYL)AMINO]-3-HYDROXY-1-PHENYL-BUTAN-2-YL] CARBAMATE
ChEMBLCHEMBL178593
DrugBank
ZINCZINC000003935926
PDB chain2qd6 Chain B Residue 404 [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]
PDB2qd6 Potent new antiviral compound shows similar inhibition and structural interactions with drug resistant mutants and wild type HIV-1 protease.
Resolution1.28 Å
Binding residue
(original residue number in PDB)
D125 G127 D129 D130 G148 G149 V150
Binding residue
(residue number reindexed from 1)
D25 G27 D29 D30 G48 G49 V50
Annotation score1
Binding affinityMOAD: Ki=2.1nM
PDBbind-CN: -logKd/Ki=8.68,Ki=2.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) D125 T126 G127
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:2qd6, PDBe:2qd6, PDBj:2qd6
PDBsum2qd6
PubMed17696515
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]