3JSW | pdb_00003jsw

Human PDE9 in complex with selective inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.212 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3JSW

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Identification of a Brain Penetrant PDE9A Inhibitor Utilizing Prospective Design and Chemical Enablement as a Rapid Lead Optimization Strategy.

Verhoest, P.R., Proulx-Lafrance, C., Corman, M., Chenard, L., Helal, C.J., Hou, X., Kleiman, R., Liu, S., Marr, E., Menniti, F.S., Schmidt, C.J., Vanase-Frawley, M., Schmidt, A.W., Williams, R.D., Nelson, F.R., Fonseca, K.R., Liras, S.

(2009) J Med Chem 52: 7946-7949

  • DOI: https://doi.org/10.1021/jm9015334
  • Primary Citation Related Structures: 
    3JSI, 3JSW

  • PubMed Abstract: 

    By use of chemical enablement and prospective design, a novel series of selective, brain penetrant PDE9A inhibitors have been identified that are capable of producing in vivo elevations of brain cGMP.

    • Organizational Affiliation: 
    • Neuroscience Chemistry, Pfizer Global Research and Development, Groton, CT 06340, USA.

Macromolecule Content 

  • Total Structure Weight: 78.61 kDa 
  • Atom Count: 5,770 
  • Modeled Residue Count: 656 
  • Deposited Residue Count: 658 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
A, B
329Homo sapiensMutation(s): 0 
Gene Names: PDE9A
EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76083 (Homo sapiens)
Explore O76083 
Go to UniProtKB:  O76083
PHAROS:  O76083
GTEx:  ENSG00000160191 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76083
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JAR

Query on JAR


Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]		6-[(3S,4S)-1-benzyl-4-methylpyrrolidin-3-yl]-1-(1-methylethyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
C20 H25 N5 O
PUGMRQMXTZPAIZ-RHSMWYFYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.212 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.278α = 90
b = 103.278β = 90
c = 270.349γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2009-12-01 
    • Deposition Author(s): Liu, S.

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description