Structure of PDB 4a6b Chain B Binding Site BS01

Receptor Information
>4a6b Chain B (length=99) Species: 12721 (Human immunodeficiency virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF
Ligand information
Ligand IDQG8
InChIInChI=1S/C44H52N4O6/c1-43(2,3)39(45-42(53)54-4)40(51)46-47(28-31-20-22-33(23-21-31)32-16-9-6-10-17-32)25-13-24-44(27-30-14-7-5-8-15-30)37(50)29-48(41(44)52)38-35-19-12-11-18-34(35)26-36(38)49/h5-12,14-23,36-39,49-50H,13,24-29H2,1-4H3,(H,45,53)(H,46,51)/t36-,37-,38+,39-,44+/m1/s1
InChIKeyYNPGDSJLNVNNFA-MIYQMFTLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC(C)(C)C(C(=O)NN(CCCC1(C(CN(C1=O)C2c3ccccc3CC2O)O)Cc4ccccc4)Cc5ccc(cc5)c6ccccc6)NC(=O)OC
CACTVS 3.370COC(=O)N[C@H](C(=O)NN(CCC[C@]1(Cc2ccccc2)[C@H](O)CN([C@@H]3[C@H](O)Cc4ccccc34)C1=O)Cc5ccc(cc5)c6ccccc6)C(C)(C)C
ACDLabs 12.01O=C(OC)NC(C(=O)NN(Cc2ccc(c1ccccc1)cc2)CCCC5(C(=O)N(C4c3c(cccc3)CC4O)CC5O)Cc6ccccc6)C(C)(C)C
CACTVS 3.370COC(=O)N[CH](C(=O)NN(CCC[C]1(Cc2ccccc2)[CH](O)CN([CH]3[CH](O)Cc4ccccc34)C1=O)Cc5ccc(cc5)c6ccccc6)C(C)(C)C
OpenEye OEToolkits 1.7.2CC(C)(C)[C@@H](C(=O)NN(CCC[C@@]1([C@@H](CN(C1=O)[C@H]2c3ccccc3C[C@H]2O)O)Cc4ccccc4)Cc5ccc(cc5)c6ccccc6)NC(=O)OC
FormulaC44 H52 N4 O6
NameMETHYL ((S)-1-(2-([1,1'-BIPHENYL]-4-YLMETHYL)-2-(3-((3S,4S)-3-BENZYL-4-HYDROXY-1-((1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL)-2-OXOPYRROLIDIN-3-YL)PROPYL)HYDRAZINYL)-3,3-DIMETHYL-1-OXOBUTAN-2-YL)CARBAMATE
ChEMBLCHEMBL2031099
DrugBank
ZINCZINC000084758148
PDB chain4a6b Chain B Residue 1200 [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]
PDB4a6b Synthesis, X-Ray Analysis, and Biological Evaluation of a New Class of Stereopure Lactam-Based HIV-1 Protease Inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		L123 D125 G127 A128 D129 G148 I150 F153 T182 V184
Binding residue
(residue number reindexed from 1)		L23 D25 G27 A28 D29 G48 I50 F53 T82 V84
Annotation score1
Binding affinityMOAD: Ki=12nM
PDBbind-CN: -logKd/Ki=8.38,Ki=4.2nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4a6b, PDBe:4a6b, PDBj:4a6b
PDBsum4a6b
PubMed22376008
UniProtP35963|POL_HV1Y2 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]