Structure of PDB 3st5 Chain B Binding Site BS01

Receptor Information

>3st5 Chain B (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE))

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: G89
• InChI: InChI=1S/C29H40N2O8S/c1-19(2)16-31(40(35,36)23-11-9-21(37-3)10-12-23)17-26(32)25(13-20-7-5-4-6-8-20)30-29(34)39-22-14-24-27(33)18-38-28(24)15-22/h4-12,19,22,24-28,32-33H,13-18H2,1-3H3,(H,30,34)/t22-,24-,25+,26-,27+,28-/m1/s1
• InChIKey: LJPOEDMTSRUIGG-RVSUYJHDSA-N
• SMILES:
  OpenEye OEToolkits 1.7.2: CC(C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@@H]2C[C@H]3[C@@H](C2)OC[C@@H]3O)O)S(=O)(=O)c4ccc(cc4)OC
  OpenEye OEToolkits 1.7.2: CC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2CC3C(C2)OCC3O)O)S(=O)(=O)c4ccc(cc4)OC
  CACTVS 3.370: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)O[C@H]3C[C@H]4OC[C@H](O)[C@H]4C3
  ACDLabs 12.01: O=S(=O)(c1ccc(OC)cc1)N(CC(C)C)CC(O)C(NC(=O)OC3CC2C(OCC2O)C3)Cc4ccccc4
  CACTVS 3.370: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](Cc2ccccc2)NC(=O)O[CH]3C[CH]4OC[CH](O)[CH]4C3
• Formula: C29 H40 N2 O8 S
• Name: (3R,3aR,5R,6aR)-3-hydroxyhexahydro-2H-cyclopenta[b]furan-5-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate
• ChEMBL: CHEMBL1817686
• ZINC: ZINC000072113044
• PDB chain: 3st5 Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3st5 Design of HIV-1 Protease Inhibitors with C3-Substituted Hexahydrocyclopentafuranyl Urethanes as P2-Ligands: Synthesis, Biological Evaluation, and Protein-Ligand X-ray Crystal Structure.
• Resolution: 1.45 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=5pM
  PDBbind-CN: -logKd/Ki=11.30,Ki=5pM

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:3st5, PDBe:3st5, PDBj:3st5
• PDBsum: 3st5
• PubMed: 21800876
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)