Fig. 1.

Binding pose of a PDE4D-NAM in the allosteric site. a Relative size and position of UCR1, UCR2, and the catalytic domain in the PDE4D polypeptide. PDE4D7 and PDE4D3 contain the UCR1 and UCR2 helices needed for dimerization through formation of a four-helix bundle. PDE4D2 lacks these helices, and so is active as a monomer. Arrows indicate the locations of the PKA phosphorylation site on UCR1 and the ERK phosphorylation sites distal to the catalytic domain. b The amino acid sequence of the UCR2 helix that closes over the active site. The sequence is conserved between PDE4D subtypes and across species with the exception of the key phenylalanine (asterisk in (a), bold and yellow highlighted in (b)) that is present in primate PDE4D UCR2. c A co-crystal structure of BPN5004 bound in the PDE4D allosteric site (PDB ID: 6BOJ). UCR2 is shown as a green ribbon structure, while catalytic domain residues are colored cyan. The pyrimidine core is clamped above and below the plane of the ring between an active site isoleucine (Ile577) and a phenylalanine (Phe613) while forming a 3.3 Å hydrogen bond to the invariant PDE active site glutamine (Gln610). Modeling of BPN14770 in the 6BOJ structure suggests that it has a similar binding pose to BPN5004. Closure of UCR2 allows the key phenylalanine selectivity residue (Phe271) to interact with the two aromatic arms of the allosteric inhibitor through an edge-on, π–π interaction to Ar1 (4.2 Å) and π–π stacking with Ar2 (3.7 Å). d Modeling of the tyrosine replacement suggests the deeper projection of the tyrosine hydroxyl group will clash sterically with the edge-on Ar2 phenyl ring (3.1 Å) and the binding energy contributed by the edge-on, π–π interaction will be lost. The larger bulk of the tyrosine hydroxyl relative to the phenylalanine is visualized by the light gray surface rendition with transparency