Structure of PDB 5yok Chain B Binding Site BS01

Receptor Information

>5yok Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: 8Z0
• InChI: InChI=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
• InChIKey: ZNVSERMHCCYPMY-JZILQDPNSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: Cc1cccc(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 3.385: COc1cccc2cc(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 3.385: COc1cccc2cc(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 2.0.6: Cc1cccc(c1CNC(=O)C2C(SCN2C(=O)C(C(Cc3ccccc3)NC(=O)C(C4CCOC4)NC(=O)c5cc6cccc(c6o5)OC)O)(C)C)C
• Formula: C41 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
• ChEMBL: CHEMBL4173216
• PDB chain: 5yok Chain A Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5yok Identification of Highly Potent Human Immunodeficiency Virus Type-1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine.
• Resolution: 0.85 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D30 V32 I47 G48 G49 I50 P81 I84
• Binding residue (residue number reindexed from 1): D25 G27 A28 D30 V32 I47 G48 G49 I50 P81 I84
• Annotation score: 1

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

External links

• PDB: RCSB:5yok, PDBe:5yok, PDBj:5yok
• PDBsum: 5yok
• PubMed: 29852069
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)