Structure of PDB 3dk1 Chain A Binding Site BS01

Receptor Information
>3dk1 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 IDG05
InChIInChI=1S/C29H40N2O8S/c1-20(2)18-31(40(34,35)24-11-9-22(36-3)10-12-24)19-26(32)25(15-21-7-5-4-6-8-21)30-29(33)39-23-16-27-28(17-23)38-14-13-37-27/h4-12,20,23,25-28,32H,13-19H2,1-3H3,(H,30,33)/t23-,25-,26+,27+,28-/m0/s1
InChIKeyJRXDKTCILCAIFM-XVYWXRPESA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)O[C@H]3C[C@H]4OCCO[C@H]4C3
OpenEye OEToolkits 1.5.0CC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2CC3C(C2)OCCO3)O)S(=O)(=O)c4ccc(cc4)OC
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](Cc2ccccc2)NC(=O)O[CH]3C[CH]4OCCO[CH]4C3
ACDLabs 10.04O=S(=O)(c1ccc(OC)cc1)N(CC(C)C)CC(O)C(NC(=O)OC2CC3OCCOC3C2)Cc4ccccc4
OpenEye OEToolkits 1.5.0CC(C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)OC2C[C@@H]3[C@H](C2)OCCO3)O)S(=O)(=O)c4ccc(cc4)OC
FormulaC29 H40 N2 O8 S
Name(4aR,6r,7aS)-hexahydro-4aH-cyclopenta[b][1,4]dioxin-6-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate
ChEMBL
DrugBank
ZINCZINC000116522216
PDB chain3dk1 Chain B 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]
PDB3dk1 Potent HIV-1 protease inhibitors incorporating meso-bicyclic urethanes as P2-ligands: structure-based design, synthesis, biological evaluation and protein-ligand X-ray studies
Resolution1.07 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=9.74,Ki=0.18nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dk1, PDBe:3dk1, PDBj:3dk1
PDBsum3dk1
PubMed18843400
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]