4NPW

Crystal structure of human PDE1B bound to inhibitor 19A (7,8-dimethoxy-N-[(2S)-1-(3-methyl-1H-pyrazol-5-yl)propan-2-yl]quinazolin-4-amine)

• PDB DOI: https://doi.org/10.2210/pdb4NPW/pdb

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


• Deposited: 2013-11-22 Released: 2014-07-16 
• Deposition Author(s): Pandit, J., Evdomikov, A., Mansour, M., Simons, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.209 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

Small-molecule phosphodiesterase probes: discovery of potent and selective CNS-penetrable quinazoline inhibitors of PDE1

Humphrey, J.M., Yang, E.X., Am Ende, C.W., Arnold, E.P., Head, J.L., Jenkinsonb, S., Lebel, L.A., Liras, S., Pandit, J., Samas, B., Vajdos, F., Simons, S.P., Evdokimova, A., Mansour, M., Menniti, F.S.

(2014) Medchemcomm 

• DOI: https://doi.org/10.1039/C4MD00113C

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: 2,872 
• 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) 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.209 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• 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
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Pandit, J., Evdomikov, A., Mansour, M., Simons, S.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations