› 2jle

X-ray diffraction
2.9Å resolution

Novel indazole nnrtis created using molecular template hybridization based on crystallographic overlays

Released:
DOI: 10.2210/pdb2jle/pdb
PDB entry 2jle coloured by chain, front view.
PDB entry 2jle coloured by chain, side view.
PDB entry 2jle coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Novel indazole non-nucleoside reverse transcriptase inhibitors using molecular hybridization based on crystallographic overlays.
Jones LH, Allan G, Barba O, Burt C, Corbau R, Dupont T, Knöchel T, Irving S, Middleton DS, Mowbray CE, Perros M, Ringrose H, Swain NA, Webster R, Westby M, Phillips C
J Med Chem 52 1219-23 (2009)
PMID: 19175319

Function and Biology Details

Reaction catalysed: 
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.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180780 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Reverse transcriptase/RNaseH Chains: A, B
Molecule details ›
Chains: A, B
Length: 566 amino acids
Theoretical weight: 65.22 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q72547 (Residues: 1-566; Coverage: 100%)
Gene name: pol
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand I15 1 x I15
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: C2221
Unit cell:
a: 117.2Å b: 154.6Å c: 155Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.267 0.261 0.351
Expression system: Escherichia coli

Quick links

Citations

6 review citations

HIV-1 NNRTIs: structural diversity, pharmacophore similarity, and implications for drug design.
Zhan et al. (2013)
5 more

7 mentions without citation

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review.
Tarasova et al. (2018)
6 more