Structure of PDB 4hdb Chain B Binding Site BS01

Receptor Information

>4hdb Chain B (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE))

PQITLWKRPLVTIKIGGQLKEALLDTGADNTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: G52
• InChI: InChI=1S/C30H40N2O9S/c1-19(2)16-32(42(35,36)22-11-9-21(37-3)10-12-22)17-25(33)24(15-20-7-5-4-6-8-20)31-30(34)40-26-18-39-29-27(26)23-13-14-38-28(23)41-29/h4-12,19,23-29,33H,13-18H2,1-3H3,(H,31,34)/t23-,24+,25-,26+,27+,28+,29+/m1/s1
• InChIKey: QWMNYFXRFHGYGS-DDGGWZRMSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CC(C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2[C@H]4CCO[C@H]4O3)O)S(=O)(=O)c5ccc(cc5)OC
  ACDLabs 12.01: O=S(=O)(c1ccc(OC)cc1)N(CC(C)C)CC(O)C(NC(=O)OC3C4C2C(OCC2)OC4OC3)Cc5ccccc5
  OpenEye OEToolkits 1.7.0: CC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2COC3C2C4CCOC4O3)O)S(=O)(=O)c5ccc(cc5)OC
  CACTVS 3.370: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](Cc2ccccc2)NC(=O)O[CH]3CO[CH]4O[CH]5OCC[CH]5[CH]34
  CACTVS 3.370: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)O[C@H]3CO[C@H]4O[C@@H]5OCC[C@@H]5[C@@H]34
• Formula: C30 H40 N2 O9 S
• Name: (3R,3aS,3bR,6aS,7aS)-octahydrodifuro[2,3-b:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate
• ChEMBL: CHEMBL1232930
• ZINC: ZINC000058631450
• PDB chain: 4hdb Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4hdb Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease.
• Resolution: 1.49 Å
• Binding residue (original residue number in PDB): D125 G127 D129 N130 G148 G149 I150
• Binding residue (residue number reindexed from 1): D25 G27 D29 N30 G48 G49 I50
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.05,Ki=8.9nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D125 T126 G127
• 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:4hdb, PDBe:4hdb, PDBj:4hdb
• PDBsum: 4hdb
• PubMed: 23298236
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)