4Y2B | pdb_00004y2b

Co-crystal structure of 3-ethyl-2-(isopropylamino)-7-(pyridin-3-yl)thieno[3,2-d]pyrimidin-4(3H)-one bound to PDE7A

PDB DOI: https://doi.org/10.2210/pdb4Y2B/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-09 Released: 2015-04-08
Deposition Author(s): Endo, Y., Kawai, K., Asano, T., Amano, S., Asanuma, Y., Sawada, K., Onodera, Y., Ueo, N., Takahashi, N., Sonoda, Y., Kamei, N., Irie, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.196 (Depositor), 0.200 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

2-(Isopropylamino)thieno[3,2-d]pyrimidin-4(3H)-one derivatives as selective phosphodiesterase 7 inhibitors with potent in vivo efficacy

Endo, Y., Kawai, K., Asano, T., Amano, S., Asanuma, Y., Sawada, K., Onodera, Y., Ueo, N., Takahashi, N., Sonoda, Y., Kamei, N., Irie, T.

(2015) Bioorg Med Chem Lett 25: 1910-1914

PubMed: 25866242 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2015.03.031
Primary Citation of Related Structures:
4Y2B

PubMed Abstract:
A new series of thienopyrimidinones is synthesized and evaluated as selective phosphodiesterase 7 (PDE7) inhibitors for the treatment of inflammatory diseases. The modification of the substituents on thienopyrimidinone revealed that an isopropylamino group at the 2-position was favorable for aqueous solubility. The introduction of 3-pyrrolidines at the 7-position resulted in good solubility, highly potent activity, and good PDE7 selectivity. Among the synthesized compounds, compound 46 exhibited the greatest inhibition of ear edema in a phorbol ester-induced mouse model.

Organizational Affiliation

Drug Research Center, Kaken Pharmaceutical Co. Ltd, 14, Shinomiya Minamigawara-cho, Yamashina, Kyoto 607-8042, Japan. Electronic address: endo_yusuke@kaken.co.jp.

Macromolecule Content

Total Structure Weight: 44.95 kDa
Atom Count: 2,903
Modelled Residue Count: 318
Deposited Residue Count: 389
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A	A	389	Homo sapiens	Mutation(s): 0 Gene Names: PDE7A EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for Q13946 (Homo sapiens) Explore Q13946 Go to UniProtKB: Q13946
PHAROS: Q13946 GTEx: ENSG00000205268
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13946
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPK Query on EPK Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	3-ethyl-2-(propan-2-ylamino)-7-(pyridin-3-yl)thieno[3,2-d]pyrimidin-4(3H)-one C₁₆ H₁₈ N₄ O S TZXUAKHZPAHOMA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [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
EPK	BindingDB: 4Y2B	IC50: 4.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.196 (Depositor), 0.200 (DCC)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.961	α = 90
b = 115.961	β = 90
c = 64.409	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-04-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-08
Type: Initial release
Version 1.1: 2015-04-29
Changes: Database references
Version 1.2: 2015-05-06
Changes: Database references
Version 1.3: 2017-10-04
Changes: Data collection, Database references, Derived calculations, Source and taxonomy
Version 1.4: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description