5XUI

Crystal structure of PDE10A in complex with 2-methyl-5-[2-([1,2,4]triazolo[1,5-a]pyrimidin-2-yl)et hyl]pyrazolo[1,5-a]pyrimidin-7-ol

• PDB DOI: https://doi.org/10.2210/pdb5XUI/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-23 Released: 2018-03-14 
• Deposition Author(s): Amano, Y., Honbou, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.272 
• R-Value Work: 0.185 
• R-Value Observed: 0.190 

Literature

Fragment-Based Discovery of Pyrimido[1,2-b]indazole PDE10A Inhibitors.

Chino, A., Seo, R., Amano, Y., Namatame, I., Hamaguchi, W., Honbou, K., Mihara, T., Yamazaki, M., Tomishima, M., Masuda, N.

(2018) Chem Pharm Bull (Tokyo) 66: 286-294

• PubMed: 29491261 
• DOI: https://doi.org/10.1248/cpb.c17-00836
• Primary Citation of Related Structures:  
  5XUI, 5XUJ


• PubMed Abstract: 
  

  In this study, we report the identification of potent pyrimidoindazoles as phosphodiesterase10A (PDE10A) inhibitors by using the method of fragment-based drug discovery (FBDD). The pyrazolopyridine derivative 2 was found to be a fragment hit compound which could occupy a part of the binding site of PDE10A enzyme by using the method of the X-ray co-crystal structure analysis. On the basis of the crystal structure of compound 2 and PDE10A protein, a number of compounds were synthesized and evaluated, by means of structure-activity relationship (SAR) studies, which culminated in the discovery of a novel pyrimidoindazole derivative 13 having good physicochemical properties.

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Organizational Affiliation: 

Drug Discovery Research, Astellas Pharma Inc.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.69 kDa 
• Atom Count: 5,275 
• Modelled Residue Count: 644 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A, B	345	Homo sapiens	Mutation(s): 0  Gene Names: PDE10A EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y233 (Homo sapiens) Explore Q9Y233  Go to UniProtKB:  Q9Y233
PHAROS:  Q9Y233 GTEx:  ENSG00000112541

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8G3	E [auth A]	2-methyl-5-[2-([1,2,4]triazolo[1,5-a]pyrimidin-2-yl)ethyl]pyrazolo[1,5-a]pyrimidin-7-ol C14 H13 N7 O MHSIAXSVRRVYRX-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.272 
• R-Value Work: 0.185 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.345	α = 90
b = 81.443	β = 90
c = 158.745	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Amano, Y., Honbou, K.

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release