Structure of PDB 3djk Chain B Binding Site BS01

Receptor Information
>3djk Chain B (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)		D125 G127 A128 D129 D130 G148 G149 I150
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 G48 G49 I50
Annotation score1
Binding affinityMOAD: Ki=26pM
PDBbind-CN: -logKd/Ki=10.59,Ki=26pM
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:3djk, PDBe:3djk, PDBj:3djk
PDBsum3djk
PubMed18783203
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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