Structure of PDB 2qd7 Chain B Binding Site BS01

Receptor Information
>2qd7 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]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPANIIGRNLLTQIGATLNF
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 chain2qd7 Chain B Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2qd7 Potent new antiviral compound shows similar inhibition and structural interactions with drug resistant mutants and wild type HIV-1 protease.
Resolution1.11 Å
Binding residue
(original residue number in PDB)
D125 G127 A128 D129 D130 G148 I150
Binding residue
(residue number reindexed from 1)
D25 G27 A28 D29 D30 G48 I50
Annotation score1
Binding affinityMOAD: Ki=0.8nM
PDBbind-CN: -logKd/Ki=9.10,Ki=0.80nM
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

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Molecular Function

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Biological Process
External links
PDB RCSB:2qd7, PDBe:2qd7, PDBj:2qd7
PDBsum2qd7
PubMed17696515
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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