5SED

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH c1c(cc2c(c1)nc(nc2N3CCOCC3)OCc4nc(cn4C)c5ccccc5)Cl, micromolar IC50=0.00213

5SED の概要

• エントリーDOI: 10.2210/pdb5sed/pdb
• Group deposition: Exploiting Structural Data for Improved On-Target Prediction in Lead Optimization (G_1002226)
• 分子名称: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A, ZINC ION, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: phosphodiesterase, pde10, hydrolase, schizophrenia, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 159763.36

構造登録者

Joseph, C.,Groebke-Zbinden, K.,Benz, J.,Schlatter, D.,Rudolph, M.G. (登録日: 2022-01-21, 公開日: 2022-10-12, 最終更新日: 2024-10-16)

主引用文献

Tosstorff, A.,Rudolph, M.G.,Cole, J.C.,Reutlinger, M.,Kramer, C.,Schaffhauser, H.,Nilly, A.,Flohr, A.,Kuhn, B.
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios.
J.Comput.Aided Mol.Des., 36:753-765, 2022

PubMed Abstract: We release a new, high quality data set of 1162 PDE10A inhibitors with experimentally determined binding affinities together with 77 PDE10A X-ray co-crystal structures from a Roche legacy project. This data set is used to compare the performance of different 2D- and 3D-machine learning (ML) as well as empirical scoring functions for predicting binding affinities with high throughput. We simulate use cases that are relevant in the lead optimization phase of early drug discovery. ML methods perform well at interpolation, but poorly in extrapolation scenarios-which are most relevant to a real-world application. Moreover, we find that investing into the docking workflow for binding pose generation using multi-template docking is rewarded with an improved scoring performance. A combination of 2D-ML and 3D scoring using a modified piecewise linear potential shows best overall performance, combining information on the protein environment with learning from existing SAR data.

PubMed: 36153472
DOI: 10.1007/s10822-022-00478-x

実験手法

X-RAY DIFFRACTION (2.32 Å)