Structure of PDB 3ndu Chain B Binding Site BS01

Receptor Information

>3ndu Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: ROC
• InChI: InChI=1S/C38H50N6O5/c1-38(2,3)43-37(49)32-20-26-14-7-8-15-27(26)22-44(32)23-33(45)30(19-24-11-5-4-6-12-24)41-36(48)31(21-34(39)46)42-35(47)29-18-17-25-13-9-10-16-28(25)40-29/h4-6,9-13,16-18,26-27,30-33,45H,7-8,14-15,19-23H2,1-3H3,(H2,39,46)(H,41,48)(H,42,47)(H,43,49)/t26-,27+,30-,31-,32-,33+/m0/s1
• InChIKey: QWAXKHKRTORLEM-UGJKXSETSA-N
• SMILES:
  ACDLabs 12.01: O=C(N)CC(NC(=O)c1nc2c(cc1)cccc2)C(=O)NC(Cc3ccccc3)C(O)CN5C(C(=O)NC(C)(C)C)CC4C(CCCC4)C5
  OpenEye OEToolkits 1.7.0: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2C[N@]1C[C@H]([C@H](Cc3ccccc3)NC(=O)[C@H](CC(=O)N)NC(=O)c4ccc5ccccc5n4)O
  OpenEye OEToolkits 1.7.0: CC(C)(C)NC(=O)C1CC2CCCCC2CN1CC(C(Cc3ccccc3)NC(=O)C(CC(=O)N)NC(=O)c4ccc5ccccc5n4)O
  CACTVS 3.370: CC(C)(C)NC(=O)[CH]1C[CH]2CCCC[CH]2CN1C[CH](O)[CH](Cc3ccccc3)NC(=O)[CH](CC(N)=O)NC(=O)c4ccc5ccccc5n4
  CACTVS 3.370: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc3ccccc3)NC(=O)[C@H](CC(N)=O)NC(=O)c4ccc5ccccc5n4
• Formula: C38 H50 N6 O5
• Name: (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide;
  Fortovase;
  SAQUINAVIR;
  RO 31-8959
• ChEMBL: CHEMBL114
• DrugBank: DB01232
• ZINC: ZINC000003914596
• PDB chain: 3ndu Chain A Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ndu Investigation of 2-Fold Disorder of Inhibitors and Relative Potency by Crystallizations of HIV-1 Protease in Ritonavir and Saquinavir Mixtures
• Resolution: 1.25 Å
• Binding residue (original residue number in PDB): D26 G28 I51 P82 I85
• Binding residue (residue number reindexed from 1): D25 G27 I50 P81 I84
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D26 T27 G28
• 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:3ndu, PDBe:3ndu, PDBj:3ndu
• PDBsum: 3ndu
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)