Structure of PDB 5ult Chain B Binding Site BS01

Receptor Information

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

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: 8FM
• InChI: InChI=1S/C30H40N2O8S/c1-19(2)15-32(41(35,36)23-11-9-22(37-3)10-12-23)16-27(33)26(13-20-7-5-4-6-8-20)31-30(34)40-28-21-14-24-25(28)18-39-29(24)38-17-21/h4-12,19,21,24-29,33H,13-18H2,1-3H3,(H,31,34)/t21-,24-,25-,26+,27-,28+,29+/m1/s1
• InChIKey: JVINLJIUYCLBEU-JBQMQJJESA-N
• SMILES:
  CACTVS 3.385: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)O[C@H]3[C@H]4CO[C@H]5OC[C@@H]3[C@H]5C4
  ACDLabs 12.01: c5c(S(=O)(N(CC(C)C)CC(O)C(NC(OC2C1COC3C(C1)C2CO3)=O)Cc4ccccc4)=O)ccc(c5)OC
  OpenEye OEToolkits 2.0.6: CC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2C3CC4C2COC4OC3)O)S(=O)(=O)c5ccc(cc5)OC
  OpenEye OEToolkits 2.0.6: CC(C)CN(C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@H]2[C@@H]3C[C@@H]4[C@H]2CO[C@@H]4OC3)O)S(=O)(=O)c5ccc(cc5)OC
  CACTVS 3.385: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](Cc2ccccc2)NC(=O)O[CH]3[CH]4CO[CH]5OC[CH]3[CH]5C4
• Formula: C30 H40 N2 O8 S
• Name: (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate
• PDB chain: 5ult Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ult Design and Development of Highly Potent HIV-1 Protease Inhibitors with a Crown-Like Oxotricyclic Core as the P2-Ligand To Combat Multidrug-Resistant HIV Variants.
• Resolution: 1.53 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 G48 G49 I50
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 G48 G49 I50
• Annotation score: 1
• Binding affinity: MOAD: Ki=0.014nM
  PDBbind-CN: -logKd/Ki=10.85,Ki=0.014nM

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:5ult, PDBe:5ult, PDBj:5ult
• PDBsum: 5ult
• PubMed: 28418652
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)