4LM3

Crystal structure of PDE10A2 with fragment ZT464

Summary for 4LM3

• Entry DOI: 10.2210/pdb4lm3/pdb
• Related: 4LKQ 4LLJ 4LLL 4LLP 4LLX 4LM0 4LM1 4LM2 4LM4
• Descriptor: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A, 1-(2,3-dihydro-1,4-benzodioxin-6-yl)ethanone, NICKEL (II) ION, ... (5 entities in total)
• Functional Keywords: fragment screening, hydrolase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: Q9Y233
• Total number of polymer chains: 2
• Total formula weight: 79557.64

Authors

Sridhar, V.,Badger, J.,Logan, C.,Chie-Leon, B.,Nienaber, V. (deposition date: 2013-07-09, release date: 2014-02-26, Last modification date: 2023-09-20)

Primary citation

Recht, M.I.,Sridhar, V.,Badger, J.,Bounaud, P.Y.,Logan, C.,Chie-Leon, B.,Nienaber, V.,Torres, F.E.
Identification and Optimization of PDE10A Inhibitors Using Fragment-Based Screening by Nanocalorimetry and X-ray Crystallography.
J Biomol Screen, 19:497-507, 2014

PubMed Abstract: Fragment-based lead discovery (FBLD) is a technique in which small, low-complexity chemical fragments of 6 to 15 heavy atoms are screened for binding to or inhibiting activity of the target. Hits are then linked and/or elaborated into tightly binding ligands, ideally yielding early lead compounds for drug discovery. Calorimetry provides a label-free method to assay binding and enzymatic activity that is unaffected by the spectroscopic properties of the sample. Conventional microcalorimetry is hampered by requiring large quantities of reagents and long measurement times. Nanocalorimeters can overcome these limitations of conventional isothermal titration calorimetry. Here we use enthalpy arrays, which are arrays of nanocalorimeters, to perform an enzyme activity-based fragment screen for competitive inhibitors of phosphodiesterase 10A (PDE10A). Two dozen fragments with KI <2 mM were identified and moved to crystal soaking trials. All soak experiments yielded high-resolution diffraction, with two-thirds of the fragments yielding high-resolution co-crystal structures with PDE10A. The structural information was used to elaborate fragment hits, yielding leads with KI <1 µM. This study shows how array calorimetry can be used as a prescreening method for fragment-based lead discovery with enzyme targets and paired successfully with an X-ray crystallography secondary screen.

PubMed: 24375910
DOI: 10.1177/1087057113516493

Experimental method

X-RAY DIFFRACTION (1.49 Å)