Structure of PDB 3tof Chain B Binding Site BS01

Receptor Information

>3tof Chain B (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE))

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: 076
• InChI: InChI=1S/C31H36N2O5/c1-21(2)28(33-27(34)20-37-24-16-10-5-11-17-24)31(36)32-25(18-22-12-6-3-7-13-22)29(35)30-26(38-30)19-23-14-8-4-9-15-23/h3-17,21,25-26,28-30,35H,18-20H2,1-2H3,(H,32,36)(H,33,34)/t25-,26+,28-,29+,30-/m0/s1
• InChIKey: ZYLARFCKPNSSDA-OUFDATPMSA-N
• SMILES:
  CACTVS 3.370: CC(C)[CH](NC(=O)COc1ccccc1)C(=O)N[CH](Cc2ccccc2)[CH](O)[CH]3O[CH]3Cc4ccccc4
  ACDLabs 12.01: O=C(NC(C(=O)NC(C(O)C2OC2Cc1ccccc1)Cc3ccccc3)C(C)C)COc4ccccc4
  CACTVS 3.370: CC(C)[C@H](NC(=O)COc1ccccc1)C(=O)N[C@@H](Cc2ccccc2)[C@@H](O)[C@H]3O[C@@H]3Cc4ccccc4
  OpenEye OEToolkits 1.7.2: CC(C)[C@@H](C(=O)N[C@@H](Cc1ccccc1)[C@H]([C@@H]2[C@H](O2)Cc3ccccc3)O)NC(=O)COc4ccccc4
  OpenEye OEToolkits 1.7.2: CC(C)C(C(=O)NC(Cc1ccccc1)C(C2C(O2)Cc3ccccc3)O)NC(=O)COc4ccccc4
• Formula: C31 H36 N2 O5
• Name: (S)-N-((1R,2S)-1-((2R,3R)-3-benzyloxiran-2-yl)-1-hydroxy-3-phenylpropan-2-yl)-3-methyl-2-(2-phenoxyacetamido)butanamide
• ZINC: ZINC000098207771
• PDB chain: 3tof Chain A Residue 100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3tof Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals.
• Resolution: 1.45 Å
• Binding residue (original residue number in PDB): R8 D25 G27 P81 V82 I84
• Binding residue (residue number reindexed from 1): R8 D25 G27 P81 V82 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:3tof, PDBe:3tof, PDBj:3tof
• PDBsum: 3tof
• PubMed: 27809253
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)