Brand  (β version)

PDB ID: 4DFG

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Ligands
Code Name Style Show Link
0JV Methyl N-[(3s,3ar,5r,6ar)-5-[[(2s,3r)-4-[(4-methoxyphenyl)sulfonyl-(2-methylpropyl)amino]-3-oxidanyl-1-phenyl-butan-2-yl]carbamoyloxy]-3,3a,4,5,6,6a-hexahydro-2h-cyclopenta[B]furan-3-yl]carbamate PoSSuM
CL Chloride ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
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Structure summary

Code : 4DFG   PDBj   RCSB PDB   PDBe
Header : hydrolase/hydrolase inhibitor
Title : Crystal Structure of Wild-type HIV-1 Protease with Cyclopentyltetrahydro- furanyl Urethanes as P2-ligand, GRL-0249A
Release Data : 2012-03-21
Compound :
mol_id molecule chains
1 Protease A,B
ec: 3.4.23.16
fragment: residues 500-598
mutation: Q7K, L33I, L63I, C67A, C95A
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1  (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 : Wang, Y.-F., Agniswamy, J., Weber, I.T.
Keywords : aspartic acid protease, HIV-1 protease inhibitor GRL-0249A, Cyclopentyltetrahydro- furanyl Urethanes P2-ligands, wild-type HIV-1 protease, hydrolase-hydrolase inhibitor complex
Exp. method : X-RAY DIFFRACTION ( 1.23 Å )
Citation :

Substituent effects on P2-cyclopentyltetrahydrofuranyl urethanes: Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors.

Ghosh, A.K.,Chapsal, B.D.,Steffey, M.  et al.
(2012)  Bioorg.Med.Chem.Lett.  22 : 2308 - 2311

PubMed: 22364812
DOI: 10.1016/j.bmcl.2012.01.061

Reaction

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
-
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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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.49 PROSITE-ProRule:PRU00405
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 PROSITE-ProRule:PRU00405
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Cofactor: Evidence: Note:
Mg(2+) ECO:0000250
Binds 2 magnesium ions for reverse transcriptase polymerase activity.
Mg(2+) ECO:0000250
Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding.
Mg(2+) ECO:0000250
Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.