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Ligands
Code Name Style Show Link
031 (3as,5r,6ar)-hexahydro-2h-cyclopenta[B]furan-5-yl [(1s,2r)-1-benzyl-2-hydroxy-3-([(4-methoxyphenyl)sulfonyl]{[(2r)-5-oxopyrrolidin-2-yl]methyl}amino)propyl]carbamate
CL Chloride ion
GOL Glycerol
NA Sodium ion
Non-standard Residues
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Modification
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Code : 3H5B   PDBj   RCSB PDB   PDBe
Header : HYDROLASE
Title : Crystal structure of wild type HIV-1 protease with novel P1'-ligand GRL-02031
Release Data : 2009-06-16
Compound :
mol_id molecule chains synonym
1 HIV-1 protease A,B Retropepsin, PR
ec: 3.4.23.16
fragment: UNP residues 501-599
mutation: Q7K, L33I, L63I, C67A, C95A
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1 (BRU ISOLATE)  (taxid:11686) HIV-1 Escherichia coli  (taxid:562)
gene: gag-pol
expression_system_strain: BL21(DE3)
expression_system_vector_type: Plasmid
expression_system_plasmid: pET11a
Authors : Tie, Y., Wang, Y.F., Weber, I.T.
Keywords : HIV-1, wild type protease, protease inhibitor, P1'-ligand, AIDS, Hydrolase
Exp. method : X-RAY DIFFRACTION ( 1.29 Å )
Citation :

Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: synthesis, biological evaluation, and protein-ligand X-ray studies.

Ghosh, A.K.,Leshchenko-Yashchuk, S.,Anderson, D.D.  et al.
(2009)  J.Med.Chem.  52 : 3902 - 3914

PubMed: 19473017
DOI: 10.1021/jm900303m

Chain : A, B
UniProt : P03367 (POL_HV1BR)
Reaction: EC: Evidence:
Physiological Direction:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 3.4.23.16 PROSITE-ProRule:PRU00275
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Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus. 3.1.26.13 -
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3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 2.7.7.49 PROSITE- ProRule:PRU00405
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a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 2.7.7.7 PROSITE- ProRule:PRU00405
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