Structure of PDB 5yok Chain A Binding Site BS01

Receptor Information
>5yok Chain A (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 ID8Z0
InChIInChI=1S/C41H48N4O8S/c1-24-11-9-12-25(2)29(24)21-42-39(49)36-41(3,4)54-23-45(36)40(50)34(46)30(19-26-13-7-6-8-14-26)43-38(48)33(28-17-18-52-22-28)44-37(47)32-20-27-15-10-16-31(51-5)35(27)53-32/h6-16,20,28,30,33-34,36,46H,17-19,21-23H2,1-5H3,(H,42,49)(H,43,48)(H,44,47)/t28-,30-,33-,34-,36+/m0/s1
InChIKeyZNVSERMHCCYPMY-JZILQDPNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cccc(c1CNC(=O)[C@@H]2C(SCN2C(=O)[C@H]([C@H](Cc3ccccc3)NC(=O)[C@H]([C@H]4CCOC4)NC(=O)c5cc6cccc(c6o5)OC)O)(C)C)C
CACTVS 3.385COc1cccc2cc(oc12)C(=O)N[CH]([CH]3CCOC3)C(=O)N[CH](Cc4ccccc4)[CH](O)C(=O)N5CSC(C)(C)[CH]5C(=O)NCc6c(C)cccc6C
CACTVS 3.385COc1cccc2cc(oc12)C(=O)N[C@@H]([C@H]3CCOC3)C(=O)N[C@@H](Cc4ccccc4)[C@H](O)C(=O)N5CSC(C)(C)[C@H]5C(=O)NCc6c(C)cccc6C
OpenEye OEToolkits 2.0.6Cc1cccc(c1CNC(=O)C2C(SCN2C(=O)C(C(Cc3ccccc3)NC(=O)C(C4CCOC4)NC(=O)c5cc6cccc(c6o5)OC)O)(C)C)C
FormulaC41 H48 N4 O8 S
Name(4R)-N-[(2,6-dimethylphenyl)methyl]-3-[(2S,3S)-3-[[(2S)-2-[(7-methoxy-1-benzofuran-2-yl)carbonylamino]-2-[(3R)-oxolan-3 -yl]ethanoyl]amino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide;
KNI-1657
ChEMBLCHEMBL4173216
DrugBank
ZINC
PDB chain5yok Chain A Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yok Identification of Highly Potent Human Immunodeficiency Virus Type-1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine.
Resolution0.85 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 D30 G48 G49 I50 I84
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 G48 G49 I50 I84
Annotation score1
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 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:5yok, PDBe:5yok, PDBj:5yok
PDBsum5yok
PubMed29852069
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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