Structure of PDB 6ixd Chain B Binding Site BS01

Receptor Information
>6ixd Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDB0F
InChIInChI=1S/C45H56N6O8S2/c1-25-18-29(46-35(53)17-11-10-16-34-38-32(23-60-34)48-44(58)50-38)19-26(2)40(25)59-22-36(54)47-31(20-27-12-6-5-7-13-27)39(55)43(57)51-24-61-45(3,4)41(51)42(56)49-37-30-15-9-8-14-28(30)21-33(37)52/h5-9,12-15,18-19,31-34,37-39,41,52,55H,10-11,16-17,20-24H2,1-4H3,(H,46,53)(H,47,54)(H,49,56)(H2,48,50,58)/t31-,32-,33+,34-,37-,38-,39-,41+/m0/s1
InChIKeyFGRIDPZSJUPACI-SOOZJBRBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1cc(cc(c1OCC(=O)NC(Cc2ccccc2)C(C(=O)N3CSC(C3C(=O)NC4c5ccccc5CC4O)(C)C)O)C)NC(=O)CCCCC6C7C(CS6)NC(=O)N7
CACTVS 3.385Cc1cc(NC(=O)CCCC[CH]2SC[CH]3NC(=O)N[CH]23)cc(C)c1OCC(=O)N[CH](Cc4ccccc4)[CH](O)C(=O)N5CSC(C)(C)[CH]5C(=O)N[CH]6[CH](O)Cc7ccccc67
OpenEye OEToolkits 2.0.7Cc1cc(cc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C(=O)N3CSC([C@H]3C(=O)N[C@H]4c5ccccc5C[C@H]4O)(C)C)O)C)NC(=O)CCCC[C@H]6[C@@H]7[C@H](CS6)NC(=O)N7
CACTVS 3.385Cc1cc(NC(=O)CCCC[C@@H]2SC[C@@H]3NC(=O)N[C@H]23)cc(C)c1OCC(=O)N[C@@H](Cc4ccccc4)[C@H](O)C(=O)N5CSC(C)(C)[C@H]5C(=O)N[C@@H]6[C@H](O)Cc7ccccc67
FormulaC45 H56 N6 O8 S2
Name(4R)-3-[(2S,3S)-3-[2-[4-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-2,6-dimethyl-phenoxy]ethanoylamino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-N-[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]-1,3-thiazolidine-4-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6ixd Chain B Residue 101 [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]
PDB6ixd Acquired Removability of Aspartic Protease Inhibitors by Direct Biotinylation.
Resolution1.0 Å
Binding residue
(original residue number in PDB)
D25 G27 A28 D29 D30 I47 G49 I50
Binding residue
(residue number reindexed from 1)
D25 G27 A28 D29 D30 I47 G49 I50
Annotation score1
Binding affinityMOAD: Ki=0.16nM
PDBbind-CN: -logKd/Ki=9.80,Ki=0.16nM
Enzymatic activity
Catalytic site (original residue number in PDB) D25 T26 G27
Catalytic site (residue number reindexed from 1) D25 T26 G27
Enzyme Commision number 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:6ixd, PDBe:6ixd, PDBj:6ixd
PDBsum6ixd
PubMed30990716
UniProtQ5RZ08

[Back to BioLiP]