Structure of PDB 3djk Chain A Binding Site BS01

Receptor Information
>3djk Chain A (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDG55
InChIInChI=1S/C27H38N2O8S/c1-20(2)16-29(38(32,33)24-11-9-22(34-3)10-12-24)17-26(30)25(15-21-7-5-4-6-8-21)28-27(31)37-23-13-14-35-19-36-18-23/h4-12,20,23,25-26,30H,13-19H2,1-3H3,(H,28,31)/t23-,25+,26-/m1/s1
InChIKeyLEJNWIFUYPPOMU-DMTNHVFBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](Cc2ccccc2)NC(=O)O[CH]3CCOCOC3
OpenEye OEToolkits 1.5.0CC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2CCOCOC2)O)S(=O)(=O)c3ccc(cc3)OC
OpenEye OEToolkits 1.5.0CC(C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@@H]2CCOCOC2)O)S(=O)(=O)c3ccc(cc3)OC
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)O[C@@H]3CCOCOC3
ACDLabs 10.04O=S(=O)(c1ccc(OC)cc1)N(CC(C)C)CC(O)C(NC(=O)OC2COCOCC2)Cc3ccccc3
FormulaC27 H38 N2 O8 S
Name(5R)-1,3-dioxepan-5-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate
ChEMBLCHEMBL492254
DrugBank
ZINCZINC000042875645
PDB chain3djk Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3djk Flexible cyclic ethers/polyethers as novel P2-ligands for HIV-1 protease inhibitors: design, synthesis, biological evaluation, and protein-ligand X-ray studies
Resolution1.0 Å
Binding residue
(original residue number in PDB)		D25 A28 D30 P81 V82
Binding residue
(residue number reindexed from 1)		D25 A28 D30 P81 V82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.59,Ki=26pM
Enzymatic activity
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:3djk, PDBe:3djk, PDBj:3djk
PDBsum3djk
PubMed18783203
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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