Structure of PDB 3dk1 Chain B Binding Site BS01

Receptor Information
>3dk1 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 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
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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)		D125 G127 A128 D129 G148 G149 I150
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 G48 G49 I50
Annotation score1
Binding affinityMOAD: Ki=0.18nM
PDBbind-CN: -logKd/Ki=9.74,Ki=0.18nM
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:3dk1, PDBe:3dk1, PDBj:3dk1
PDBsum3dk1
PubMed18843400
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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