5W6E

PDE1b complexed with compound 3S

• PDB DOI: https://doi.org/10.2210/pdb5W6E/pdb

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


• Deposited: 2017-06-16 Released: 2018-05-30 
• Deposition Author(s): Vajdos, F.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Discovery of Potent and Selective Periphery-Restricted Quinazoline Inhibitors of the Cyclic Nucleotide Phosphodiesterase PDE1.

Humphrey, J.M., Movsesian, M., Am Ende, C.W., Becker, S.L., Chappie, T.A., Jenkinson, S., Liras, J.L., Liras, S., Orozco, C., Pandit, J., Vajdos, F.F., Vandeput, F., Yang, E., Menniti, F.S.

(2018) J Med Chem 61: 4635-4640

• PubMed: 29718668 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b00374
• Primary Citation of Related Structures:  
  5W6E


• PubMed Abstract: 
  

  We disclose the discovery and X-ray cocrystal data of potent, selective quinazoline inhibitors of PDE1. Inhibitor ( S)-3 readily attains free plasma concentrations above PDE1 IC ₅₀ values and has restricted brain access. The racemic compound 3 inhibits >75% of PDE hydrolytic activity in soluble samples of human myocardium, consistent with heightened PDE1 activity in this tissue. These compounds represent promising new tools to probe the value of PDE1 inhibition in the treatment of cardiovascular disease.

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Organizational Affiliation: 

Pfizer World Wide Research and Development , Eastern Point Road , Groton , Connecticut 06340 , United States.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 42.55 kDa 
• Atom Count: 2,924 
• Modelled Residue Count: 321 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B	A	369	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0NY	D [auth A]	7,8-dimethoxy-N-[(2S)-1-(3-methyl-1H-pyrazol-5-yl)propan-2-yl]quinazolin-4-amine C17 H21 N5 O2 JTROLECZHRVLFM-JTQLQIEISA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0NY	Binding MOAD:  5W6E	IC50: 9.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.782	α = 90
b = 88.782	β = 90
c = 134.806	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Vajdos, F.F.

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2018-06-06
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations