PDBsum entry 4mrz

Hydrolase/hydrolase inhibitor

PDB id: 4mrz

Contents

Protein chains

330 a.a.

Ligands

2ZV

Metals

_NI ×4

Waters ×334

PDB id:

4mrz

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of pde10a2 with fragment zt0429 (4-methyl-3- nitropyridin-2-amine)

Structure:

Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10a. Chain: a, b. Fragment: catalytic domain, unp residues 439-779. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pde10a. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.58Å R-factor: 0.208 R-free: 0.236

Authors:

V.Sridhar,J.Badger,C.Logan,B.Chie-Leon,V.Nienaber

Key ref:

M.I.Recht et al. (2014). Identification and optimization of PDE10A inhibitors using fragment-based screening by nanocalorimetry and X-ray crystallography. J Biomol Screen, 19, 497-507. PubMed id: 24375910 DOI: 10.1177/1087057113516493

Date:

17-Sep-13 Release date: 14-May-14

Protein chains

Q9Y233  (PDE10_HUMAN) -  cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A from Homo sapiens

Seq: 779 a.a.

Struc: 330 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.4.17 - 3',5'-cyclic-nucleotide phosphodiesterase.
• Reaction: a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1177/1087057113516493

J Biomol Screen 19:497-507 (2014)

PubMed id: 24375910

Identification and optimization of PDE10A inhibitors using fragment-based screening by nanocalorimetry and X-ray crystallography.

M.I.Recht, V.Sridhar, J.Badger, P.Y.Bounaud, C.Logan, B.Chie-Leon, V.Nienaber, F.E.Torres.

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.