5UOY

Crystal structure of human PDE1B catalytic domain in complex with inhibitor 16j (6-(4-Methoxybenzyl)-9-((tetrahydro-2H-pyran-4-yl)methyl)-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one)

PDB DOI: https://doi.org/10.2210/pdb5UOY/pdb

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

Deposited: 2017-02-01 Released: 2017-04-26
Deposition Author(s): Cedervall, E.P., Allerston, C.K., Xu, R., Sridhar, V., Barker, R., Aertgeerts, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.189 (Depositor), 0.200 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of Selective Phosphodiesterase 1 Inhibitors with Memory Enhancing Properties.

Dyck, B., Branstetter, B., Gharbaoui, T., Hudson, A.R., Breitenbucher, J.G., Gomez, L., Botrous, I., Marrone, T., Barido, R., Allerston, C.K., Cedervall, E.P., Xu, R., Sridhar, V., Barker, R., Aertgeerts, K., Schmelzer, K., Neul, D., Lee, D., Massari, M.E., Andersen, C.B., Sebring, K., Zhou, X., Petroski, R., Limberis, J., Augustin, M., Chun, L.E., Edwards, T.E., Peters, M., Tabatabaei, A.

(2017) J Med Chem 60: 3472-3483

PubMed: 28406621 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.7b00302
Primary Citation of Related Structures:
5UOY, 5UP0, 5UWF

PubMed Abstract:
A series of potent thienotriazolopyrimidinone-based PDE1 inhibitors was discovered. X-ray crystal structures of example compounds from this series in complex with the catalytic domain of PDE1B and PDE10A were determined, allowing optimization of PDE1B potency and PDE selectivity. Reduction of hERG affinity led to greater than a 3000-fold selectivity for PDE1B over hERG. 6-(4-Methoxybenzyl)-9-((tetrahydro-2H-pyran-4-yl)methyl)-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one was identified as an orally bioavailable and brain penetrating PDE1B enzyme inhibitor with potent memory-enhancing effects in a rat model of object recognition memory.

Organizational Affiliation

Dart Neuroscience LLC , 12278 Scripps Summit Drive, San Diego, California 92131, United States.

Macromolecule Content

Total Structure Weight: 42.3 kDa
Atom Count: 2,805
Modelled Residue Count: 321
Deposited Residue Count: 361
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B	A	361	Homo sapiens	Mutation(s): 0 Gene Names: PDE1B, PDE1B1, PDES1B EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q01064 (Homo sapiens) Explore Q01064 Go to UniProtKB: Q01064
PHAROS: Q01064 GTEx: ENSG00000123360
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01064
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8HM Query on 8HM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	6-[(4-methoxyphenyl)methyl]-9-[(oxan-4-yl)methyl]-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one C₂₄ H₂₇ N₅ O₃ S BQOIGGMSKKKZRK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
8HM	BindingDB: 5UOY	IC50: min: 27, max: 100 (nM) from 2 assay(s)
8HM	BindingDB: 5UOY	EC50: 100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.189 (Depositor), 0.200 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.507	α = 90
b = 87.507	β = 90
c = 134.714	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-04-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-26
Type: Initial release
Version 1.1: 2017-05-10
Changes: Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description