Macromolecule Content

Total Structure Weight: 78.49 kDa
Atom Count: 5489
Modelled Residue Count: 656
Deposited Residue Count: 658
Unique protein chains: 1

3JSI

Human phosphodiesterase 9 in complex with inhibitor

PDB DOI: 10.2210/pdb3JSI/pdb

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

Deposited: 2009-09-10 Released: 2009-12-01
Deposition Author(s): Liu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.218
R-Value Work: 0.205
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 19919087 Search on PubMed
DOI: 10.1021/jm9015334
Primary Citation of Related Structures:
3JSI, 3JSW

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	A, B	329	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O76083
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WTC Query on WTC Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A]	E [auth A], H [auth B]	6-benzyl-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one C₁₇ H₁₈ N₄ O FVOYQCUKGQGDKH-UHFFFAOYSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
WTC	PDBBind: 3JSI	IC50: 2.1 (nM) from 1 assay(s)
WTC	BindingDB: 3JSI	IC50: min: 0.8, max: 2.1 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.218
R-Value Work: 0.205
R-Value Observed: 0.205
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.099	α = 90
b = 104.099	β = 90
c = 271.04	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2009-09-10
Released Date: 2009-12-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.