Primary Citation PubMed: 10441122
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Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity.
(2009) BMC Bioinformatics 10
PubMed: 19671127 | PubMedCentral: PMC2739202 | DOI: 10.1186/1471-2105-10-245
Two of the RNase ligands display a bicephal structure ( 1QHC and 1JN4 ligands), one part based on the classic purine-like scaffolds, and the other based on a pyrimidine-like scaffolds, the two parts b... ing connected by a poly-phosphate chain linker.
Publication Year: 2009
Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: an X-ray crystallographic study.
(2009) Biopolymers 91
PubMed: 19191310 | PubMedCentral: PMC2816359 | DOI: 10.1002/bip.21158
Table I Categorized Binding of 5′-Phosphoadenosine-Based Inhibitors to RNase A Ring Stacking Partners (B 2 Subsite) N -glycosidic Torsion Angle, χ b P 1 Subsite Representatives His119 ... otamer a Adenine Subfragment Range in Degrees Ligand Compound PDB Entry Protein Chain c Reference Class Ia A Pentacyclic ring 293–314 (high- anti ) 5 ′ -P α pA 1Z6S A(A), B 26 pA-3 ′ -p 1O0F A, B 22 pA-2 ′ -p 1O0O B 22 Class Ib A Pentacyclic ring <293 ( anti /high- anti ) Not 5 ′ -P α pA 1Z6S A(B) 26 Class II A Hexacyclic ring 31–88 ( syn ) 5 ′ -P β ppA 1O0H A 22 ppA-3 ′ -p 1AFK A, B 20 ppA-2 ′ -p 1AFL A, B 20 dUppA 1JN4 A 27 pdUppA-3 ′ -p 1QHC A, B 21 pdTppA-3 ′ -p 1U1B A, B 28 Class III B Both rings 277 (high-anti) 2′-P pA-2′-p 1O0O A 22 a For rotamer A, χ 1 ≈ 150° and χ 2 ≈ −100°; for rotamer B, χ 1 ≈ −70° and χ 2 ≈ −60°.
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