Structure of PDB 2pyn Chain B Binding Site BS01

Receptor Information

>2pyn Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWQRPLVTIKIGGQLKEALLDTGADNTVLEEMSLPGAWKPKMIGGI
GGFIKVRQYDQILIEICGHKVIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 1UN
• InChI: InChI=1S/C32H45N3O4S/c1-21-25(15-10-16-28(21)36)30(38)33-26(20-40-24-13-6-5-7-14-24)29(37)19-35-18-23-12-9-8-11-22(23)17-27(35)31(39)34-32(2,3)4/h5-7,10,13-16,22-23,26-27,29,36-37H,8-9,11-12,17-20H2,1-4H3,(H,33,38)(H,34,39)/t22-,23+,26-,27-,29+/m0/s1
• InChIKey: QAGYKUNXZHXKMR-HKWSIXNMSA-N
• SMILES:
  CACTVS 3.341: Cc1c(O)cccc1C(=O)N[CH](CSc2ccccc2)[CH](O)CN3C[CH]4CCCC[CH]4C[CH]3C(=O)NC(C)(C)C
  CACTVS 3.341: Cc1c(O)cccc1C(=O)N[C@@H](CSc2ccccc2)[C@H](O)CN3C[C@H]4CCCC[C@H]4C[C@H]3C(=O)NC(C)(C)C
  ACDLabs 10.04: O=C(c1cccc(O)c1C)NC(CSc2ccccc2)C(O)CN4C(C(=O)NC(C)(C)C)CC3CCCCC3C4
  OpenEye OEToolkits 1.5.0: Cc1c(cccc1O)C(=O)NC(CSc2ccccc2)C(CN3CC4CCCCC4CC3C(=O)NC(C)(C)C)O
  OpenEye OEToolkits 1.5.0: Cc1c(cccc1O)C(=O)N[C@@H](CSc2ccccc2)[C@@H](C[N@@]3C[C@H]4CCCC[C@H]4C[C@H]3C(=O)NC(C)(C)C)O
• Formula: C32 H45 N3 O4 S
• Name: 2-[2-HYDROXY-3-(3-HYDROXY-2-METHYL-BENZOYLAMINO)-4-PHENYL SULFANYL-BUTYL]-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID TERT-BUTYLAMIDE;
  NELFINAVIR MESYLATE AG1343
• ChEMBL: CHEMBL584
• DrugBank: DB00220
• ZINC: ZINC000003833846
• PDB chain: 2pyn Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2pyn Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): D25 G27 G49 I50
• Binding residue (residue number reindexed from 1): D25 G27 G49 I50
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.57,Kd=27nM

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:2pyn, PDBe:2pyn, PDBj:2pyn
• PDBsum: 2pyn
• PubMed: 17977555
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)