Structure of PDB 3aid Chain B Binding Site BS01

Receptor Information
>3aid 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]
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPVEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDARQ
InChIInChI=1S/C30H37N3O4/c1-30(2,3)37-29(36)31-26(20-23-14-8-5-9-15-23)27(34)22-33(4,21-24-16-10-6-11-17-24)32-28(35)25-18-12-7-13-19-25/h5-19,26-27,34H,20-22H2,1-4H3,(H-,31,32,35,36)/p+1/t26-,27-,33+/m0/s1
InChIKeyKTCIZECZUWZDHY-ZTMGNVKNSA-O
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(OC(C)(C)C)NC(Cc1ccccc1)C(O)C[N+](NC(=O)c2ccccc2)(Cc3ccccc3)C
OpenEye OEToolkits 1.5.0CC(C)(C)OC(=O)NC(Cc1ccccc1)C(C[N+](C)(Cc2ccccc2)NC(=O)c3ccccc3)O
OpenEye OEToolkits 1.5.0CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)[C@H](C[N@@+](C)(Cc2ccccc2)NC(=O)c3ccccc3)O
CACTVS 3.341CC(C)(C)OC(=O)N[CH](Cc1ccccc1)[CH](O)C[N+](C)(Cc2ccccc2)NC(=O)c3ccccc3
CACTVS 3.341CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)C[N@@+](C)(Cc2ccccc2)NC(=O)c3ccccc3
FormulaC30 H38 N3 O4
NameBENZOYLAMINO-BENZYL-METHYL-[2-HYDROXY-3-[1-METHYL-ETHYL-OXY-N-FORMAMIDYL]-4-PHENYL-BUTYL]-AMMONIUM
ChEMBL
DrugBank
ZINCZINC000257842732
PDB chain3aid Chain A Residue 401 [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]
PDB3aid A new class of HIV-1 protease inhibitor: the crystallographic structure, inhibition and chemical synthesis of an aminimide peptide isostere.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D25 G27 G48 G49 I50
Binding residue
(residue number reindexed from 1)		D25 G27 G48 G49 I50
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.86,Ki=137nM
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:3aid, PDBe:3aid, PDBj:3aid
PDBsum3aid
PubMed8894111
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]